Starting phenix.real_space_refine on Thu Sep 18 16:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hpk_52332/09_2025/9hpk_52332.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hpk_52332/09_2025/9hpk_52332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hpk_52332/09_2025/9hpk_52332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hpk_52332/09_2025/9hpk_52332.map" model { file = "/net/cci-nas-00/data/ceres_data/9hpk_52332/09_2025/9hpk_52332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hpk_52332/09_2025/9hpk_52332.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 11560 2.51 5 N 2862 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17705 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3113 Classifications: {'peptide': 396} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 379} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3102 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 382} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 399, 3102 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 382} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3155 Chain: "C" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3102 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 380} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 397, 3096 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 380} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 397, 3096 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 380} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3154 Chain: "W" Number of atoms: 1310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 bond proxies already assigned to first conformer: 1333 Chain: "X" Number of atoms: 1310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 bond proxies already assigned to first conformer: 1333 Chain: "Y" Number of atoms: 1310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 bond proxies already assigned to first conformer: 1333 Chain: "Z" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1301 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE B 578 " occ=0.64 ... (20 atoms not shown) pdb=" CZ BPHE B 578 " occ=0.36 residue: pdb=" N APHE D 578 " occ=0.56 ... (20 atoms not shown) pdb=" CZ BPHE D 578 " occ=0.43 Time building chain proxies: 6.38, per 1000 atoms: 0.36 Number of scatterers: 17705 At special positions: 0 Unit cell: (112.336, 129.682, 138.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 3170 8.00 N 2862 7.00 C 11560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 777 " distance=2.04 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 777 " distance=2.03 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 777 " distance=2.04 Simple disulfide: pdb=" SG CYS D 722 " - pdb=" SG CYS D 777 " distance=2.03 Simple disulfide: pdb=" SG CYS W 67 " - pdb=" SG CYS W 77 " distance=2.03 Simple disulfide: pdb=" SG CYS X 67 " - pdb=" SG CYS X 77 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 67 " - pdb=" SG CYS Y 77 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 67 " - pdb=" SG CYS Z 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 62.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 418 through 421 removed outlier: 3.602A pdb=" N GLU A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 421' Processing helix chain 'A' and resid 425 through 439 removed outlier: 3.604A pdb=" N ASP A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 524 through 548 Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 599 through 628 Processing helix chain 'A' and resid 639 through 645 removed outlier: 3.528A pdb=" N LEU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 668 through 681 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 710 through 717 Processing helix chain 'A' and resid 746 through 760 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 792 through 828 removed outlier: 3.815A pdb=" N VAL A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 800 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 438 Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 524 through 548 Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.591A pdb=" N GLU B 552 " --> pdb=" O SER B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 Processing helix chain 'B' and resid 599 through 621 Processing helix chain 'B' and resid 623 through 630 Processing helix chain 'B' and resid 639 through 646 removed outlier: 3.544A pdb=" N LEU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.550A pdb=" N GLU B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.708A pdb=" N SER B 680 " --> pdb=" O SER B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 710 through 718 removed outlier: 3.601A pdb=" N GLN B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 760 Processing helix chain 'B' and resid 761 through 772 Processing helix chain 'B' and resid 796 through 828 removed outlier: 3.830A pdb=" N PHE B 800 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 418 through 421 removed outlier: 3.612A pdb=" N GLU C 421 " --> pdb=" O GLU C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 421' Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'C' and resid 524 through 548 Processing helix chain 'C' and resid 576 through 589 Processing helix chain 'C' and resid 599 through 628 Processing helix chain 'C' and resid 639 through 646 removed outlier: 3.853A pdb=" N LEU C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 668 through 680 removed outlier: 3.842A pdb=" N SER C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 710 through 718 removed outlier: 3.867A pdb=" N GLN C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 760 Processing helix chain 'C' and resid 761 through 772 Processing helix chain 'C' and resid 792 through 795 Processing helix chain 'C' and resid 796 through 828 removed outlier: 3.865A pdb=" N PHE C 800 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 418 through 421 removed outlier: 4.101A pdb=" N GLU D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 425 through 438 removed outlier: 3.586A pdb=" N ASP D 429 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 524 through 548 Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.778A pdb=" N GLU D 552 " --> pdb=" O SER D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 589 Processing helix chain 'D' and resid 599 through 621 Processing helix chain 'D' and resid 623 through 630 Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 657 through 665 removed outlier: 3.507A pdb=" N GLU D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 681 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 710 through 718 removed outlier: 3.526A pdb=" N GLN D 718 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 760 Processing helix chain 'D' and resid 761 through 771 Processing helix chain 'D' and resid 792 through 795 Processing helix chain 'D' and resid 796 through 828 removed outlier: 3.805A pdb=" N PHE D 800 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 30 Processing helix chain 'W' and resid 95 through 105 Processing helix chain 'W' and resid 105 through 128 removed outlier: 4.204A pdb=" N GLU W 126 " --> pdb=" O ILE W 122 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE W 127 " --> pdb=" O ALA W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 161 removed outlier: 3.987A pdb=" N LEU W 136 " --> pdb=" O HIS W 132 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA W 161 " --> pdb=" O ILE W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 210 removed outlier: 3.722A pdb=" N TYR W 181 " --> pdb=" O GLY W 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 30 Processing helix chain 'X' and resid 95 through 105 Processing helix chain 'X' and resid 105 through 128 Processing helix chain 'X' and resid 132 through 161 removed outlier: 3.676A pdb=" N LEU X 136 " --> pdb=" O HIS X 132 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA X 161 " --> pdb=" O ILE X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 208 removed outlier: 3.711A pdb=" N TYR X 181 " --> pdb=" O GLY X 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU X 208 " --> pdb=" O ARG X 204 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 30 Processing helix chain 'Y' and resid 95 through 105 Processing helix chain 'Y' and resid 105 through 128 removed outlier: 3.917A pdb=" N GLU Y 126 " --> pdb=" O ILE Y 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE Y 127 " --> pdb=" O ALA Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 161 removed outlier: 3.680A pdb=" N LEU Y 136 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 210 removed outlier: 3.596A pdb=" N TYR Y 181 " --> pdb=" O GLY Y 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 30 Processing helix chain 'Z' and resid 95 through 105 Processing helix chain 'Z' and resid 105 through 128 removed outlier: 4.081A pdb=" N GLU Z 126 " --> pdb=" O ILE Z 122 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE Z 127 " --> pdb=" O ALA Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 161 removed outlier: 3.831A pdb=" N LEU Z 136 " --> pdb=" O HIS Z 132 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 209 removed outlier: 3.685A pdb=" N TYR Z 181 " --> pdb=" O GLY Z 177 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE Z 188 " --> pdb=" O ALA Z 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 442 through 446 removed outlier: 3.571A pdb=" N VAL A 478 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 479 " --> pdb=" O GLY A 737 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY A 737 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 481 " --> pdb=" O GLY A 735 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 735 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 442 through 446 removed outlier: 3.571A pdb=" N VAL A 478 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 479 " --> pdb=" O GLY A 737 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY A 737 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 481 " --> pdb=" O GLY A 735 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 735 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A 498 " --> pdb=" O TYR A 736 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 653 removed outlier: 6.606A pdb=" N ALA A 650 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A 707 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 652 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N GLU A 709 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N PHE A 704 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS A 507 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 442 through 446 removed outlier: 6.484A pdb=" N ILE B 397 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER B 445 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 399 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 476 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AA7, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AA8, first strand: chain 'B' and resid 498 through 500 removed outlier: 4.134A pdb=" N MET B 498 " --> pdb=" O TYR B 736 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 650 through 652 removed outlier: 6.356A pdb=" N ALA B 650 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU B 707 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 652 " --> pdb=" O LEU B 707 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N GLU B 709 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N PHE B 704 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS B 507 " --> pdb=" O PHE B 704 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 504 " --> pdb=" O VAL B 727 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 396 through 401 removed outlier: 6.755A pdb=" N ILE C 397 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER C 445 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL C 399 " --> pdb=" O SER C 445 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 409 through 410 Processing sheet with id=AB3, first strand: chain 'C' and resid 477 through 482 removed outlier: 9.512A pdb=" N ALA C 477 " --> pdb=" O PRO C 741 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA C 479 " --> pdb=" O ALA C 739 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 739 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C 481 " --> pdb=" O GLY C 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 477 through 482 removed outlier: 9.512A pdb=" N ALA C 477 " --> pdb=" O PRO C 741 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA C 479 " --> pdb=" O ALA C 739 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 739 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU C 481 " --> pdb=" O GLY C 737 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET C 498 " --> pdb=" O TYR C 736 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 650 through 652 removed outlier: 6.562A pdb=" N ALA C 650 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU C 707 " --> pdb=" O ALA C 650 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY C 652 " --> pdb=" O LEU C 707 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLU C 709 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N PHE C 704 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS C 507 " --> pdb=" O PHE C 704 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C 504 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 442 through 446 removed outlier: 6.775A pdb=" N ILE D 397 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER D 445 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 399 " --> pdb=" O SER D 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 476 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ALA D 477 " --> pdb=" O PRO D 741 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA D 479 " --> pdb=" O ALA D 739 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA D 739 " --> pdb=" O ALA D 479 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 481 " --> pdb=" O GLY D 737 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 442 through 446 removed outlier: 6.775A pdb=" N ILE D 397 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER D 445 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 399 " --> pdb=" O SER D 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 476 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ALA D 477 " --> pdb=" O PRO D 741 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA D 479 " --> pdb=" O ALA D 739 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA D 739 " --> pdb=" O ALA D 479 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 481 " --> pdb=" O GLY D 737 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET D 498 " --> pdb=" O TYR D 736 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AB9, first strand: chain 'D' and resid 686 through 687 removed outlier: 8.352A pdb=" N THR D 687 " --> pdb=" O TYR D 651 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR D 653 " --> pdb=" O THR D 687 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA D 650 " --> pdb=" O ALA D 705 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 707 " --> pdb=" O ALA D 650 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY D 652 " --> pdb=" O LEU D 707 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLU D 709 " --> pdb=" O GLY D 652 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N LEU D 654 " --> pdb=" O GLU D 709 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N PHE D 704 " --> pdb=" O LYS D 507 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS D 507 " --> pdb=" O PHE D 704 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE D 504 " --> pdb=" O VAL D 727 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'X' and resid 77 through 79 Processing sheet with id=AC3, first strand: chain 'Y' and resid 34 through 36 removed outlier: 3.506A pdb=" N THR Y 66 " --> pdb=" O LYS Y 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 77 through 79 1123 hydrogen bonds defined for protein. 3249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2733 1.31 - 1.43: 5127 1.43 - 1.56: 10034 1.56 - 1.69: 0 1.69 - 1.81: 185 Bond restraints: 18079 Sorted by residual: bond pdb=" CA SER B 580 " pdb=" CB SER B 580 " ideal model delta sigma weight residual 1.531 1.410 0.121 1.56e-02 4.11e+03 6.04e+01 bond pdb=" C CYS B 593 " pdb=" O CYS B 593 " ideal model delta sigma weight residual 1.237 1.312 -0.075 1.50e-02 4.44e+03 2.50e+01 bond pdb=" C ALA B 587 " pdb=" O ALA B 587 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.18e+01 bond pdb=" C GLY B 576 " pdb=" O GLY B 576 " ideal model delta sigma weight residual 1.232 1.190 0.042 9.10e-03 1.21e+04 2.13e+01 bond pdb=" CA PHE B 575 " pdb=" C PHE B 575 " ideal model delta sigma weight residual 1.526 1.473 0.053 1.20e-02 6.94e+03 1.93e+01 ... (remaining 18074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 24122 2.21 - 4.43: 237 4.43 - 6.64: 45 6.64 - 8.86: 9 8.86 - 11.07: 2 Bond angle restraints: 24415 Sorted by residual: angle pdb=" CA BPHE B 578 " pdb=" C BPHE B 578 " pdb=" O BPHE B 578 " ideal model delta sigma weight residual 120.42 112.29 8.13 1.06e+00 8.90e-01 5.88e+01 angle pdb=" CA APHE B 578 " pdb=" C APHE B 578 " pdb=" O APHE B 578 " ideal model delta sigma weight residual 120.42 112.68 7.74 1.06e+00 8.90e-01 5.33e+01 angle pdb=" N MET B 589 " pdb=" CA MET B 589 " pdb=" C MET B 589 " ideal model delta sigma weight residual 113.20 105.27 7.93 1.21e+00 6.83e-01 4.29e+01 angle pdb=" CA GLY B 576 " pdb=" C GLY B 576 " pdb=" O GLY B 576 " ideal model delta sigma weight residual 122.28 115.88 6.40 1.00e+00 1.00e+00 4.10e+01 angle pdb=" C GLN B 590 " pdb=" CA GLN B 590 " pdb=" CB GLN B 590 " ideal model delta sigma weight residual 111.26 121.90 -10.64 1.67e+00 3.59e-01 4.06e+01 ... (remaining 24410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9512 17.94 - 35.87: 884 35.87 - 53.81: 126 53.81 - 71.75: 20 71.75 - 89.68: 9 Dihedral angle restraints: 10551 sinusoidal: 4072 harmonic: 6479 Sorted by residual: dihedral pdb=" CB CYS D 722 " pdb=" SG CYS D 722 " pdb=" SG CYS D 777 " pdb=" CB CYS D 777 " ideal model delta sinusoidal sigma weight residual 93.00 171.19 -78.19 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS C 722 " pdb=" SG CYS C 722 " pdb=" SG CYS C 777 " pdb=" CB CYS C 777 " ideal model delta sinusoidal sigma weight residual 93.00 156.71 -63.71 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS A 722 " pdb=" SG CYS A 722 " pdb=" SG CYS A 777 " pdb=" CB CYS A 777 " ideal model delta sinusoidal sigma weight residual 93.00 149.30 -56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 10548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2565 0.081 - 0.162: 155 0.162 - 0.243: 8 0.243 - 0.324: 1 0.324 - 0.405: 1 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA ASN B 573 " pdb=" N ASN B 573 " pdb=" C ASN B 573 " pdb=" CB ASN B 573 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA GLU B 574 " pdb=" N GLU B 574 " pdb=" C GLU B 574 " pdb=" CB GLU B 574 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU A 500 " pdb=" CB LEU A 500 " pdb=" CD1 LEU A 500 " pdb=" CD2 LEU A 500 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 2727 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BPHE B 578 " -0.044 2.00e-02 2.50e+03 9.21e-02 8.49e+01 pdb=" C BPHE B 578 " 0.159 2.00e-02 2.50e+03 pdb=" O BPHE B 578 " -0.059 2.00e-02 2.50e+03 pdb=" N ASN B 579 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA APHE B 578 " -0.041 2.00e-02 2.50e+03 8.58e-02 7.37e+01 pdb=" C APHE B 578 " 0.148 2.00e-02 2.50e+03 pdb=" O APHE B 578 " -0.055 2.00e-02 2.50e+03 pdb=" N ASN B 579 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 577 " 0.034 2.00e-02 2.50e+03 7.11e-02 5.06e+01 pdb=" C ILE B 577 " -0.123 2.00e-02 2.50e+03 pdb=" O ILE B 577 " 0.046 2.00e-02 2.50e+03 pdb=" N APHE B 578 " 0.043 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2774 2.76 - 3.29: 16631 3.29 - 3.83: 29863 3.83 - 4.36: 34891 4.36 - 4.90: 61906 Nonbonded interactions: 146065 Sorted by model distance: nonbonded pdb=" OD1 ASN Z 160 " pdb=" O HOH Z 401 " model vdw 2.221 3.040 nonbonded pdb=" O PRO D 550 " pdb=" NH2 ARG W 209 " model vdw 2.233 3.120 nonbonded pdb=" O PHE B 519 " pdb=" OH TYR B 620 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASN X 160 " pdb=" O HOH X 401 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR Y 30 " pdb=" OG SER Y 179 " model vdw 2.252 3.040 ... (remaining 146060 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 395 through 412 or (resid 413 through 416 and (name N or n \ ame CA or name C or name O or name CB )) or resid 417 or (resid 418 and (name N \ or name CA or name C or name O or name CB )) or resid 419 through 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 438 or (resid 439 and (name N or name CA or name C or name O or name CB )) or \ resid 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) \ or resid 442 through 448 or (resid 449 and (name N or name CA or name C or name \ O or name CB )) or resid 450 through 455 or (resid 456 and (name N or name CA o \ r name C or name O or name CB )) or resid 457 or (resid 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 or (resid 460 through 461 and \ (name N or name CA or name C or name O or name CB )) or resid 462 through 553 or \ resid 571 through 577 or resid 579 through 592 or resid 594 through 662 or (res \ id 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thr \ ough 827 or (resid 828 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'B' and (resid 395 through 438 or (resid 439 and (name N or name CA or na \ me C or name O or name CB )) or resid 440 through 455 or (resid 456 and (name N \ or name CA or name C or name O or name CB )) or resid 457 or (resid 458 and (nam \ e N or name CA or name C or name O or name CB )) or resid 459 or (resid 460 thro \ ugh 461 and (name N or name CA or name C or name O or name CB )) or resid 462 th \ rough 509 or resid 514 through 553 or resid 571 through 577 or resid 579 through \ 592 or resid 594 through 628 or resid 636 through 662 or (resid 663 and (name N \ or name CA or name C or name O or name CB )) or resid 664 through 827 or (resid \ 828 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 395 through 412 or (resid 413 through 416 and (name N or n \ ame CA or name C or name O or name CB )) or resid 417 or (resid 418 and (name N \ or name CA or name C or name O or name CB )) or resid 419 through 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) or \ resid 442 through 448 or (resid 449 and (name N or name CA or name C or name O o \ r name CB )) or resid 450 through 455 or (resid 456 and (name N or name CA or na \ me C or name O or name CB )) or resid 457 through 459 or (resid 460 through 461 \ and (name N or name CA or name C or name O or name CB )) or resid 462 through 50 \ 9 or resid 514 through 553 or resid 571 through 577 or resid 579 through 592 or \ resid 594 through 827 or (resid 828 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'D' and (resid 395 through 412 or (resid 413 through 416 and (name N or n \ ame CA or name C or name O or name CB )) or resid 417 or (resid 418 and (name N \ or name CA or name C or name O or name CB )) or resid 419 through 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) or \ resid 442 through 448 or (resid 449 and (name N or name CA or name C or name O o \ r name CB )) or resid 450 through 460 or (resid 461 and (name N or name CA or na \ me C or name O or name CB )) or resid 462 through 577 or resid 579 through 592 o \ r resid 594 through 628 or resid 636 through 662 or (resid 663 and (name N or na \ me CA or name C or name O or name CB )) or resid 664 through 828)) } ncs_group { reference = (chain 'W' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 through 104 or resid 106 through 147 or resid 149 through 210)) selection = (chain 'X' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 through 104 or resid 106 through 147 or resid 149 through 210)) selection = (chain 'Y' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 through 104 or resid 106 through 147 or resid 149 through 210)) selection = (chain 'Z' and (resid 6 through 104 or resid 106 through 147 or resid 149 throug \ h 210)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 18087 Z= 0.218 Angle : 0.595 11.073 24431 Z= 0.365 Chirality : 0.042 0.405 2730 Planarity : 0.005 0.092 2988 Dihedral : 13.563 89.682 6393 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 19.67 % 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: 1.44 (0.19), residues: 2195 helix: 2.21 (0.14), residues: 1330 sheet: -1.87 (0.36), residues: 208 loop : -0.68 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 828 TYR 0.023 0.001 TYR A 715 PHE 0.022 0.001 PHE X 182 TRP 0.019 0.001 TRP B 770 HIS 0.004 0.001 HIS W 205 Details of bonding type rmsd covalent geometry : bond 0.00382 (18079) covalent geometry : angle 0.59419 (24415) SS BOND : bond 0.00491 ( 8) SS BOND : angle 1.27833 ( 16) hydrogen bonds : bond 0.14352 ( 1111) hydrogen bonds : angle 5.27529 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 768 ASN cc_start: 0.8322 (m110) cc_final: 0.7997 (m110) outliers start: 0 outliers final: 1 residues processed: 322 average time/residue: 0.6104 time to fit residues: 219.3989 Evaluate side-chains 273 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 594 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN B 751 ASN C 713 ASN C 760 GLN C 768 ASN D 623 ASN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101589 restraints weight = 40371.692| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.12 r_work: 0.3219 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18087 Z= 0.154 Angle : 0.519 7.720 24431 Z= 0.276 Chirality : 0.041 0.175 2730 Planarity : 0.004 0.053 2988 Dihedral : 3.912 52.711 2439 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.18 % Allowed : 9.28 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 1.75 (0.19), residues: 2195 helix: 2.52 (0.14), residues: 1333 sheet: -1.55 (0.37), residues: 189 loop : -0.85 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 455 TYR 0.018 0.001 TYR C 432 PHE 0.021 0.001 PHE X 182 TRP 0.013 0.001 TRP B 770 HIS 0.005 0.001 HIS W 205 Details of bonding type rmsd covalent geometry : bond 0.00370 (18079) covalent geometry : angle 0.51912 (24415) SS BOND : bond 0.00145 ( 8) SS BOND : angle 0.79499 ( 16) hydrogen bonds : bond 0.04564 ( 1111) hydrogen bonds : angle 3.97011 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 677 TYR cc_start: 0.7284 (t80) cc_final: 0.6962 (t80) REVERT: B 638 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: B 687 THR cc_start: 0.6768 (m) cc_final: 0.5935 (p) REVERT: B 688 LYS cc_start: 0.8428 (mptt) cc_final: 0.7773 (mppt) REVERT: B 692 ASP cc_start: 0.7214 (m-30) cc_final: 0.7011 (m-30) REVERT: B 823 ARG cc_start: 0.5172 (OUTLIER) cc_final: 0.4782 (mtm110) REVERT: C 672 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: D 638 GLU cc_start: 0.7227 (tm-30) cc_final: 0.7014 (tm-30) REVERT: D 648 GLU cc_start: 0.7559 (pm20) cc_final: 0.7345 (pm20) REVERT: X 131 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.5590 (mmt180) REVERT: Y 58 MET cc_start: 0.7660 (tpp) cc_final: 0.7440 (tpp) REVERT: Z 106 ILE cc_start: 0.7637 (tp) cc_final: 0.7333 (tp) outliers start: 22 outliers final: 6 residues processed: 306 average time/residue: 0.6076 time to fit residues: 206.9734 Evaluate side-chains 279 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 55 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 751 ASN C 760 GLN C 768 ASN C 795 ASN Y 160 ASN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099278 restraints weight = 50107.401| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.68 r_work: 0.3108 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18087 Z= 0.141 Angle : 0.487 6.194 24431 Z= 0.260 Chirality : 0.040 0.185 2730 Planarity : 0.004 0.052 2988 Dihedral : 3.699 21.737 2437 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.61 % Allowed : 11.27 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 1.91 (0.19), residues: 2195 helix: 2.66 (0.14), residues: 1333 sheet: -1.45 (0.38), residues: 176 loop : -0.84 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 455 TYR 0.018 0.001 TYR A 715 PHE 0.019 0.001 PHE W 73 TRP 0.011 0.001 TRP B 770 HIS 0.004 0.001 HIS W 205 Details of bonding type rmsd covalent geometry : bond 0.00339 (18079) covalent geometry : angle 0.48721 (24415) SS BOND : bond 0.00102 ( 8) SS BOND : angle 0.51783 ( 16) hydrogen bonds : bond 0.04175 ( 1111) hydrogen bonds : angle 3.82593 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 677 TYR cc_start: 0.7152 (t80) cc_final: 0.6813 (t80) REVERT: B 638 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: B 641 GLU cc_start: 0.7941 (mp0) cc_final: 0.7741 (pm20) REVERT: B 687 THR cc_start: 0.6719 (m) cc_final: 0.5907 (p) REVERT: B 688 LYS cc_start: 0.8356 (mptt) cc_final: 0.7735 (mppt) REVERT: B 692 ASP cc_start: 0.7188 (m-30) cc_final: 0.6973 (m-30) REVERT: B 823 ARG cc_start: 0.4953 (OUTLIER) cc_final: 0.4592 (mtm110) REVERT: C 672 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: D 638 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6896 (tm-30) REVERT: D 648 GLU cc_start: 0.7296 (pm20) cc_final: 0.6961 (pm20) REVERT: X 65 ARG cc_start: 0.6063 (mtt90) cc_final: 0.5375 (mtm180) REVERT: X 131 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5431 (mmt180) REVERT: Y 58 MET cc_start: 0.7597 (tpp) cc_final: 0.7299 (tpp) REVERT: Y 69 LEU cc_start: 0.7445 (tp) cc_final: 0.7238 (mp) REVERT: Z 106 ILE cc_start: 0.7392 (tp) cc_final: 0.7111 (tp) REVERT: Z 204 ARG cc_start: 0.6768 (mtt180) cc_final: 0.6408 (mtp85) outliers start: 30 outliers final: 12 residues processed: 288 average time/residue: 0.6359 time to fit residues: 203.7326 Evaluate side-chains 284 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain X residue 131 ARG Chi-restraints excluded: chain Y residue 192 MET Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 132 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 768 ASN D 623 ASN ** Z 60 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 = 0.3837 r_free = 0.3837 target = 0.158221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098507 restraints weight = 44115.079| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.47 r_work: 0.3097 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18087 Z= 0.166 Angle : 0.505 6.194 24431 Z= 0.268 Chirality : 0.041 0.195 2730 Planarity : 0.004 0.051 2988 Dihedral : 3.748 20.799 2437 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.09 % Allowed : 11.96 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 1.88 (0.18), residues: 2195 helix: 2.63 (0.14), residues: 1333 sheet: -1.37 (0.38), residues: 176 loop : -0.87 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 455 TYR 0.020 0.001 TYR W 174 PHE 0.020 0.001 PHE X 182 TRP 0.012 0.001 TRP B 770 HIS 0.005 0.001 HIS Z 205 Details of bonding type rmsd covalent geometry : bond 0.00407 (18079) covalent geometry : angle 0.50529 (24415) SS BOND : bond 0.00237 ( 8) SS BOND : angle 0.51719 ( 16) hydrogen bonds : bond 0.04309 ( 1111) hydrogen bonds : angle 3.79246 ( 3249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7818 (m-30) cc_final: 0.7618 (t0) REVERT: A 677 TYR cc_start: 0.7144 (t80) cc_final: 0.6836 (t80) REVERT: B 638 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 651 TYR cc_start: 0.8682 (p90) cc_final: 0.8100 (p90) REVERT: B 687 THR cc_start: 0.6818 (m) cc_final: 0.6045 (p) REVERT: B 688 LYS cc_start: 0.8394 (mptt) cc_final: 0.7775 (mppt) REVERT: B 692 ASP cc_start: 0.7125 (m-30) cc_final: 0.6894 (m-30) REVERT: B 823 ARG cc_start: 0.4948 (OUTLIER) cc_final: 0.4569 (mtm110) REVERT: C 672 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: D 638 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6939 (tm-30) REVERT: D 646 GLN cc_start: 0.5559 (pp30) cc_final: 0.5039 (pp30) REVERT: D 648 GLU cc_start: 0.7299 (pm20) cc_final: 0.6872 (pm20) REVERT: X 65 ARG cc_start: 0.6197 (mtt90) cc_final: 0.5985 (mtt90) REVERT: X 131 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.5446 (mmt180) REVERT: Y 58 MET cc_start: 0.7593 (tpp) cc_final: 0.7266 (tpp) REVERT: Z 106 ILE cc_start: 0.7423 (tp) cc_final: 0.7142 (tp) REVERT: Z 204 ARG cc_start: 0.6762 (mtt180) cc_final: 0.6398 (mtp85) outliers start: 39 outliers final: 17 residues processed: 304 average time/residue: 0.5971 time to fit residues: 202.0123 Evaluate side-chains 289 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain X residue 131 ARG Chi-restraints excluded: chain Y residue 192 MET Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 768 ASN D 623 ASN ** Z 60 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 = 0.3833 r_free = 0.3833 target = 0.157898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097877 restraints weight = 45034.833| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.47 r_work: 0.3097 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18087 Z= 0.174 Angle : 0.517 8.530 24431 Z= 0.272 Chirality : 0.042 0.338 2730 Planarity : 0.004 0.052 2988 Dihedral : 3.780 21.098 2437 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.88 % Allowed : 13.14 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 1.89 (0.18), residues: 2195 helix: 2.61 (0.14), residues: 1336 sheet: -1.28 (0.41), residues: 161 loop : -0.85 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 455 TYR 0.020 0.001 TYR A 715 PHE 0.020 0.002 PHE X 182 TRP 0.014 0.001 TRP B 770 HIS 0.005 0.001 HIS Z 205 Details of bonding type rmsd covalent geometry : bond 0.00430 (18079) covalent geometry : angle 0.51678 (24415) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.58421 ( 16) hydrogen bonds : bond 0.04343 ( 1111) hydrogen bonds : angle 3.78348 ( 3249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: A 677 TYR cc_start: 0.7184 (t80) cc_final: 0.6788 (t80) REVERT: B 574 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7602 (mm-30) REVERT: B 638 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: B 651 TYR cc_start: 0.8696 (p90) cc_final: 0.8138 (p90) REVERT: B 687 THR cc_start: 0.6897 (m) cc_final: 0.6196 (p) REVERT: B 823 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.4553 (mtm110) REVERT: C 436 LYS cc_start: 0.7402 (mmmm) cc_final: 0.7188 (mtpt) REVERT: C 672 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: D 638 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6969 (tm-30) REVERT: D 646 GLN cc_start: 0.5754 (pp30) cc_final: 0.5211 (pp30) REVERT: D 648 GLU cc_start: 0.7301 (pm20) cc_final: 0.6883 (pm20) REVERT: X 65 ARG cc_start: 0.6205 (mtt90) cc_final: 0.6001 (mtt90) REVERT: X 131 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5415 (mmt180) REVERT: Y 58 MET cc_start: 0.7614 (tpp) cc_final: 0.7226 (tpp) REVERT: Z 65 ARG cc_start: 0.6715 (ptp90) cc_final: 0.6400 (ptp90) REVERT: Z 204 ARG cc_start: 0.6748 (mtt180) cc_final: 0.6378 (mtp85) outliers start: 35 outliers final: 22 residues processed: 286 average time/residue: 0.6321 time to fit residues: 200.3686 Evaluate side-chains 292 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 117 MET Chi-restraints excluded: chain X residue 131 ARG Chi-restraints excluded: chain Y residue 192 MET Chi-restraints excluded: chain Z residue 58 MET Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 36 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 135 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 768 ASN D 623 ASN ** Z 60 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 = 0.3849 r_free = 0.3849 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100284 restraints weight = 52239.306| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.55 r_work: 0.3121 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18087 Z= 0.122 Angle : 0.471 7.771 24431 Z= 0.250 Chirality : 0.040 0.226 2730 Planarity : 0.004 0.050 2988 Dihedral : 3.635 20.888 2437 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.39 % Allowed : 14.65 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 2.13 (0.19), residues: 2195 helix: 2.81 (0.14), residues: 1341 sheet: -1.23 (0.41), residues: 160 loop : -0.80 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 828 TYR 0.019 0.001 TYR A 715 PHE 0.011 0.001 PHE X 182 TRP 0.014 0.001 TRP B 770 HIS 0.006 0.001 HIS Y 60 Details of bonding type rmsd covalent geometry : bond 0.00290 (18079) covalent geometry : angle 0.47085 (24415) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.46266 ( 16) hydrogen bonds : bond 0.03788 ( 1111) hydrogen bonds : angle 3.64448 ( 3249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: A 677 TYR cc_start: 0.7213 (t80) cc_final: 0.6811 (t80) REVERT: B 574 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7617 (mm-30) REVERT: B 638 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: B 651 TYR cc_start: 0.8692 (p90) cc_final: 0.8128 (p90) REVERT: B 687 THR cc_start: 0.6820 (m) cc_final: 0.6089 (p) REVERT: B 823 ARG cc_start: 0.5081 (OUTLIER) cc_final: 0.4620 (mtm110) REVERT: C 672 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: D 455 ARG cc_start: 0.6952 (ttt90) cc_final: 0.6672 (tpt-90) REVERT: D 638 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7115 (tm-30) REVERT: D 646 GLN cc_start: 0.5777 (pp30) cc_final: 0.5274 (pp30) REVERT: D 648 GLU cc_start: 0.7303 (pm20) cc_final: 0.6832 (pm20) REVERT: D 713 ASN cc_start: 0.7953 (t0) cc_final: 0.7748 (t0) REVERT: D 719 ARG cc_start: 0.6188 (mtp-110) cc_final: 0.5595 (mtm180) REVERT: Y 31 ASP cc_start: 0.6815 (m-30) cc_final: 0.6600 (p0) REVERT: Y 58 MET cc_start: 0.7559 (tpp) cc_final: 0.7155 (tpp) REVERT: Z 106 ILE cc_start: 0.7423 (tp) cc_final: 0.7134 (tp) REVERT: Z 204 ARG cc_start: 0.6670 (mtt180) cc_final: 0.6312 (mtp85) outliers start: 26 outliers final: 15 residues processed: 285 average time/residue: 0.6833 time to fit residues: 215.2473 Evaluate side-chains 281 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 412 LYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 126 optimal weight: 0.4980 chunk 161 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 ASN B 751 ASN C 768 ASN D 623 ASN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100196 restraints weight = 53223.499| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.57 r_work: 0.3111 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18087 Z= 0.132 Angle : 0.479 7.542 24431 Z= 0.254 Chirality : 0.040 0.229 2730 Planarity : 0.004 0.050 2988 Dihedral : 3.624 19.931 2437 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.39 % Allowed : 14.91 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 2.15 (0.19), residues: 2195 helix: 2.83 (0.14), residues: 1341 sheet: -1.23 (0.41), residues: 160 loop : -0.80 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 828 TYR 0.021 0.001 TYR W 174 PHE 0.021 0.001 PHE W 73 TRP 0.015 0.001 TRP B 770 HIS 0.004 0.001 HIS W 205 Details of bonding type rmsd covalent geometry : bond 0.00319 (18079) covalent geometry : angle 0.47853 (24415) SS BOND : bond 0.00125 ( 8) SS BOND : angle 0.45523 ( 16) hydrogen bonds : bond 0.03869 ( 1111) hydrogen bonds : angle 3.65318 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 264 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: A 677 TYR cc_start: 0.7157 (t80) cc_final: 0.6777 (t80) REVERT: B 574 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7524 (mm-30) REVERT: B 638 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: B 651 TYR cc_start: 0.8692 (p90) cc_final: 0.8148 (p90) REVERT: B 687 THR cc_start: 0.6957 (m) cc_final: 0.6307 (p) REVERT: C 672 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: D 455 ARG cc_start: 0.6962 (ttt90) cc_final: 0.6632 (tpt-90) REVERT: D 638 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7204 (tm-30) REVERT: X 65 ARG cc_start: 0.6213 (mtt90) cc_final: 0.6008 (mtt90) REVERT: Y 31 ASP cc_start: 0.6842 (m-30) cc_final: 0.6621 (p0) REVERT: Y 58 MET cc_start: 0.7569 (tpp) cc_final: 0.7222 (tpp) REVERT: Z 106 ILE cc_start: 0.7394 (tp) cc_final: 0.7093 (tp) REVERT: Z 204 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6291 (mtp85) outliers start: 26 outliers final: 14 residues processed: 274 average time/residue: 0.6684 time to fit residues: 203.0615 Evaluate side-chains 276 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 ASN B 751 ASN C 768 ASN D 623 ASN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096214 restraints weight = 41736.022| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.25 r_work: 0.3095 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18087 Z= 0.191 Angle : 0.525 7.319 24431 Z= 0.276 Chirality : 0.042 0.265 2730 Planarity : 0.004 0.051 2988 Dihedral : 3.789 20.100 2437 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.56 % Allowed : 15.29 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 1.95 (0.19), residues: 2195 helix: 2.66 (0.14), residues: 1335 sheet: -1.28 (0.39), residues: 174 loop : -0.83 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 719 TYR 0.022 0.002 TYR A 715 PHE 0.019 0.002 PHE B 497 TRP 0.018 0.001 TRP B 770 HIS 0.005 0.001 HIS Z 205 Details of bonding type rmsd covalent geometry : bond 0.00475 (18079) covalent geometry : angle 0.52465 (24415) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.48644 ( 16) hydrogen bonds : bond 0.04412 ( 1111) hydrogen bonds : angle 3.76839 ( 3249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: A 677 TYR cc_start: 0.7154 (t80) cc_final: 0.6773 (t80) REVERT: B 638 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: B 651 TYR cc_start: 0.8674 (p90) cc_final: 0.8108 (p90) REVERT: B 687 THR cc_start: 0.6918 (m) cc_final: 0.6249 (p) REVERT: C 672 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: D 455 ARG cc_start: 0.6942 (ttt90) cc_final: 0.6561 (tpt-90) REVERT: D 638 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7258 (tm-30) REVERT: D 648 GLU cc_start: 0.7380 (pm20) cc_final: 0.7175 (pm20) REVERT: Y 31 ASP cc_start: 0.6813 (m-30) cc_final: 0.6542 (p0) REVERT: Y 58 MET cc_start: 0.7521 (tpp) cc_final: 0.7222 (tpp) REVERT: Z 204 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6333 (mtp85) outliers start: 29 outliers final: 17 residues processed: 277 average time/residue: 0.6429 time to fit residues: 197.9264 Evaluate side-chains 278 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 126 optimal weight: 0.0170 chunk 156 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN B 751 ASN C 768 ASN D 623 ASN D 718 GLN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099492 restraints weight = 55153.676| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.74 r_work: 0.3111 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18087 Z= 0.118 Angle : 0.467 7.331 24431 Z= 0.249 Chirality : 0.039 0.209 2730 Planarity : 0.004 0.050 2988 Dihedral : 3.611 19.698 2437 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.18 % Allowed : 16.09 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 2.22 (0.19), residues: 2195 helix: 2.89 (0.14), residues: 1341 sheet: -1.22 (0.41), residues: 160 loop : -0.79 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 719 TYR 0.021 0.001 TYR A 715 PHE 0.021 0.001 PHE W 73 TRP 0.017 0.001 TRP B 770 HIS 0.004 0.001 HIS W 60 Details of bonding type rmsd covalent geometry : bond 0.00277 (18079) covalent geometry : angle 0.46734 (24415) SS BOND : bond 0.00128 ( 8) SS BOND : angle 0.42979 ( 16) hydrogen bonds : bond 0.03708 ( 1111) hydrogen bonds : angle 3.61127 ( 3249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 677 TYR cc_start: 0.7125 (t80) cc_final: 0.6771 (t80) REVERT: B 574 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7582 (mm-30) REVERT: B 638 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: B 651 TYR cc_start: 0.8643 (p90) cc_final: 0.8087 (p90) REVERT: B 687 THR cc_start: 0.7072 (m) cc_final: 0.6469 (p) REVERT: C 672 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: D 455 ARG cc_start: 0.6902 (ttt90) cc_final: 0.6577 (tpt-90) REVERT: D 574 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6785 (mp0) REVERT: D 638 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7315 (tm-30) REVERT: D 648 GLU cc_start: 0.7414 (pm20) cc_final: 0.7206 (pm20) REVERT: D 713 ASN cc_start: 0.7960 (t0) cc_final: 0.7750 (t0) REVERT: D 719 ARG cc_start: 0.6179 (mtp-110) cc_final: 0.5635 (mtm180) REVERT: Y 58 MET cc_start: 0.7566 (tpp) cc_final: 0.7272 (tpp) REVERT: Z 106 ILE cc_start: 0.7409 (tp) cc_final: 0.7121 (tp) REVERT: Z 204 ARG cc_start: 0.6694 (mtt180) cc_final: 0.6334 (mtp85) outliers start: 22 outliers final: 14 residues processed: 272 average time/residue: 0.6810 time to fit residues: 205.5453 Evaluate side-chains 276 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 168 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN B 751 ASN C 768 ASN D 623 ASN D 718 GLN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099082 restraints weight = 45968.246| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.52 r_work: 0.3117 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18087 Z= 0.138 Angle : 0.485 7.238 24431 Z= 0.256 Chirality : 0.040 0.211 2730 Planarity : 0.004 0.052 2988 Dihedral : 3.627 18.672 2437 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.02 % Allowed : 16.63 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 2.18 (0.19), residues: 2195 helix: 2.85 (0.14), residues: 1339 sheet: -1.11 (0.40), residues: 173 loop : -0.79 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 719 TYR 0.024 0.001 TYR W 174 PHE 0.014 0.001 PHE B 497 TRP 0.019 0.001 TRP B 770 HIS 0.004 0.001 HIS W 205 Details of bonding type rmsd covalent geometry : bond 0.00336 (18079) covalent geometry : angle 0.48477 (24415) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.41468 ( 16) hydrogen bonds : bond 0.03897 ( 1111) hydrogen bonds : angle 3.63728 ( 3249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 641 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: A 677 TYR cc_start: 0.7151 (t80) cc_final: 0.6816 (t80) REVERT: B 574 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7557 (mm-30) REVERT: B 638 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 651 TYR cc_start: 0.8687 (p90) cc_final: 0.8150 (p90) REVERT: B 687 THR cc_start: 0.7035 (m) cc_final: 0.6448 (p) REVERT: C 648 GLU cc_start: 0.7182 (pm20) cc_final: 0.6917 (pm20) REVERT: C 672 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: D 455 ARG cc_start: 0.6999 (ttt90) cc_final: 0.6663 (tpt-90) REVERT: D 638 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7213 (tm-30) REVERT: D 648 GLU cc_start: 0.7396 (pm20) cc_final: 0.7173 (pm20) REVERT: Y 58 MET cc_start: 0.7558 (tpp) cc_final: 0.7250 (tpp) REVERT: Z 65 ARG cc_start: 0.6754 (ptp90) cc_final: 0.6542 (ptp90) REVERT: Z 106 ILE cc_start: 0.7393 (tp) cc_final: 0.7092 (tp) REVERT: Z 150 ILE cc_start: 0.7460 (mt) cc_final: 0.7164 (tp) REVERT: Z 204 ARG cc_start: 0.6627 (mtt180) cc_final: 0.6260 (mtp85) outliers start: 19 outliers final: 14 residues processed: 272 average time/residue: 0.6810 time to fit residues: 205.5194 Evaluate side-chains 271 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 129 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 213 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 168 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 186 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 ASN B 751 ASN C 768 ASN D 623 ASN D 713 ASN D 718 GLN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099522 restraints weight = 49513.191| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.56 r_work: 0.3117 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18087 Z= 0.130 Angle : 0.478 7.222 24431 Z= 0.253 Chirality : 0.040 0.199 2730 Planarity : 0.004 0.052 2988 Dihedral : 3.610 19.089 2437 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.39 % Allowed : 16.42 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.67 % 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: 2.17 (0.19), residues: 2195 helix: 2.84 (0.14), residues: 1347 sheet: -1.16 (0.41), residues: 160 loop : -0.84 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 719 TYR 0.020 0.001 TYR A 715 PHE 0.019 0.001 PHE W 73 TRP 0.019 0.001 TRP B 770 HIS 0.004 0.001 HIS W 205 Details of bonding type rmsd covalent geometry : bond 0.00311 (18079) covalent geometry : angle 0.47774 (24415) SS BOND : bond 0.00132 ( 8) SS BOND : angle 0.39056 ( 16) hydrogen bonds : bond 0.03803 ( 1111) hydrogen bonds : angle 3.61896 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8021.00 seconds wall clock time: 136 minutes 55.41 seconds (8215.41 seconds total)