Starting phenix.real_space_refine on Wed Nov 19 07:38:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b70_7062/11_2025/6b70_7062.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b70_7062/11_2025/6b70_7062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b70_7062/11_2025/6b70_7062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b70_7062/11_2025/6b70_7062.map" model { file = "/net/cci-nas-00/data/ceres_data/6b70_7062/11_2025/6b70_7062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b70_7062/11_2025/6b70_7062.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 14201 2.51 5 N 3718 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22192 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7748 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 897} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7677 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1624 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Chain: "D" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1624 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Chain: "F" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "a" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "c" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 111 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASN C 207 " occ=0.84 ... (6 atoms not shown) pdb=" ND2 ASN C 207 " occ=0.84 residue: pdb=" N THR D 23 " occ=0.95 ... (5 atoms not shown) pdb=" CG2 THR D 23 " occ=0.95 residue: pdb=" N LYS D 46 " occ=0.91 ... (7 atoms not shown) pdb=" NZ LYS D 46 " occ=0.91 residue: pdb=" N GLU D 106 " occ=0.95 ... (7 atoms not shown) pdb=" OE2 GLU D 106 " occ=0.95 residue: pdb=" N ASN E 207 " occ=0.84 ... (6 atoms not shown) pdb=" ND2 ASN E 207 " occ=0.84 residue: pdb=" N THR F 23 " occ=0.95 ... (5 atoms not shown) pdb=" CG2 THR F 23 " occ=0.95 residue: pdb=" N LYS F 46 " occ=0.91 ... (7 atoms not shown) pdb=" NZ LYS F 46 " occ=0.91 residue: pdb=" N GLU F 106 " occ=0.95 ... (7 atoms not shown) pdb=" OE2 GLU F 106 " occ=0.95 Time building chain proxies: 5.22, per 1000 atoms: 0.24 Number of scatterers: 22192 At special positions: 0 Unit cell: (162.023, 163.096, 150.22, 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 70 16.00 O 4203 8.00 N 3718 7.00 C 14201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 11 " distance=2.05 Simple disulfide: pdb=" SG CYS c 6 " - pdb=" SG CYS c 11 " distance=2.04 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: 1.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 35 sheets defined 33.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.613A pdb=" N PHE A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 167 removed outlier: 4.058A pdb=" N GLN A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 192 removed outlier: 3.613A pdb=" N LYS A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.015A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.811A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.730A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.640A pdb=" N GLU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.668A pdb=" N LEU A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 4.024A pdb=" N VAL A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 516 removed outlier: 3.942A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 4.475A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.744A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 720 Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.696A pdb=" N MET A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 823 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.586A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.524A pdb=" N PHE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 913 removed outlier: 3.833A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.527A pdb=" N THR A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 929 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 944 removed outlier: 4.294A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.490A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.883A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 116 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.848A pdb=" N ALA B 161 " --> pdb=" O HIS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.816A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 3.732A pdb=" N ASP B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.794A pdb=" N LYS B 217 " --> pdb=" O PRO B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.726A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.804A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.842A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.610A pdb=" N TYR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.650A pdb=" N LEU B 384 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 385 " --> pdb=" O GLU B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 385' Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.764A pdb=" N PHE B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 470 through 471 No H-bonds generated for 'chain 'B' and resid 470 through 471' Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.906A pdb=" N VAL B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.567A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 4.405A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 585 " --> pdb=" O PHE B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 585' Processing helix chain 'B' and resid 586 through 614 removed outlier: 3.580A pdb=" N SER B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 Processing helix chain 'B' and resid 655 through 673 removed outlier: 3.739A pdb=" N ASN B 671 " --> pdb=" O MET B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.673A pdb=" N ALA B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 707 removed outlier: 4.011A pdb=" N VAL B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 708 through 721 Proline residue: B 717 - end of helix Processing helix chain 'B' and resid 734 through 754 removed outlier: 3.710A pdb=" N ASP B 747 " --> pdb=" O GLN B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.669A pdb=" N GLN B 762 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 763 " --> pdb=" O PRO B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 801 through 823 removed outlier: 3.806A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 855 through 874 Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.822A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.523A pdb=" N LYS B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 removed outlier: 3.592A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1002 removed outlier: 4.369A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B1002 " --> pdb=" O PHE B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.875A pdb=" N THR C 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.828A pdb=" N THR E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.595A pdb=" N THR E 139 " --> pdb=" O SER E 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 183 through 188 removed outlier: 3.561A pdb=" N TYR F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 3.548A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.934A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP A 553 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 731 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 621 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.770A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR A 779 " --> pdb=" O HIS A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 69 removed outlier: 4.107A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 258 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 148 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 150 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 152 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 137 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 303 through 304 removed outlier: 5.290A pdb=" N ILE B 304 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 492 removed outlier: 3.533A pdb=" N TYR B 500 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.366A pdb=" N LEU B 559 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 832 through 840 removed outlier: 4.109A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN B 844 " --> pdb=" O THR B 797 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.743A pdb=" N GLN C 6 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLY C 19 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.548A pdb=" N THR C 116 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.548A pdb=" N THR C 116 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.318A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.318A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AC1, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AC2, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.516A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR D 88 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 119 removed outlier: 5.544A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AC5, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'E' and resid 6 through 10 Processing sheet with id=AC7, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.597A pdb=" N TRP E 39 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER E 53 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE E 37 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.757A pdb=" N ARG E 101 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.658A pdb=" N GLY E 147 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS E 148 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 188 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 150 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.658A pdb=" N GLY E 147 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS E 148 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 188 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 150 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR E 184 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 161 through 162 removed outlier: 4.144A pdb=" N TYR E 202 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AD4, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.224A pdb=" N LEU F 12 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 54 through 55 removed outlier: 6.397A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR F 98 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.551A pdb=" N ASN F 138 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER F 178 " --> pdb=" O CYS F 135 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 147 through 151 979 hydrogen bonds defined for protein. 2724 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: 4.80 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7117 1.34 - 1.48: 6041 1.48 - 1.61: 9456 1.61 - 1.75: 0 1.75 - 1.88: 117 Bond restraints: 22731 Sorted by residual: bond pdb=" C PHE A 317 " pdb=" N PRO A 318 " ideal model delta sigma weight residual 1.334 1.293 0.041 1.11e-02 8.12e+03 1.35e+01 bond pdb=" CB VAL A 186 " pdb=" CG2 VAL A 186 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.00e+00 bond pdb=" CB ASN A 591 " pdb=" CG ASN A 591 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.27e+00 bond pdb=" CB TRP A 908 " pdb=" CG TRP A 908 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.12e+00 bond pdb=" CB VAL E 51 " pdb=" CG2 VAL E 51 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.96e+00 ... (remaining 22726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28995 2.46 - 4.92: 1533 4.92 - 7.38: 223 7.38 - 9.84: 49 9.84 - 12.30: 6 Bond angle restraints: 30806 Sorted by residual: angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 109.79 118.44 -8.65 1.56e+00 4.11e-01 3.08e+01 angle pdb=" C PHE E 154 " pdb=" N PRO E 155 " pdb=" CA PRO E 155 " ideal model delta sigma weight residual 127.00 139.30 -12.30 2.40e+00 1.74e-01 2.63e+01 angle pdb=" C CYS c 6 " pdb=" N CYS c 7 " pdb=" CA CYS c 7 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C ASP A 586 " pdb=" N PRO A 587 " pdb=" CA PRO A 587 " ideal model delta sigma weight residual 119.84 113.61 6.23 1.25e+00 6.40e-01 2.48e+01 angle pdb=" C PHE E 154 " pdb=" N PRO E 155 " pdb=" CD PRO E 155 " ideal model delta sigma weight residual 120.60 110.32 10.28 2.20e+00 2.07e-01 2.18e+01 ... (remaining 30801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 12874 17.57 - 35.15: 698 35.15 - 52.72: 128 52.72 - 70.29: 9 70.29 - 87.87: 10 Dihedral angle restraints: 13719 sinusoidal: 5545 harmonic: 8174 Sorted by residual: dihedral pdb=" CA PRO B 772 " pdb=" C PRO B 772 " pdb=" N ASP B 773 " pdb=" CA ASP B 773 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER B 171 " pdb=" C SER B 171 " pdb=" N PRO B 172 " pdb=" CA PRO B 172 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO C 131 " pdb=" C PRO C 131 " pdb=" N LEU C 132 " pdb=" CA LEU C 132 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 13716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2179 0.059 - 0.118: 937 0.118 - 0.177: 218 0.177 - 0.236: 35 0.236 - 0.294: 7 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CB ILE B 319 " pdb=" CA ILE B 319 " pdb=" CG1 ILE B 319 " pdb=" CG2 ILE B 319 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB VAL A 153 " pdb=" CA VAL A 153 " pdb=" CG1 VAL A 153 " pdb=" CG2 VAL A 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA GLU A 503 " pdb=" N GLU A 503 " pdb=" C GLU A 503 " pdb=" CB GLU A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3373 not shown) Planarity restraints: 3965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 57 " 0.060 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO B 58 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 156 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO C 157 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU a 16 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LEU a 16 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU a 16 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU a 17 " 0.019 2.00e-02 2.50e+03 ... (remaining 3962 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2521 2.73 - 3.27: 21158 3.27 - 3.82: 37805 3.82 - 4.36: 43136 4.36 - 4.90: 74345 Nonbonded interactions: 178965 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG1 THR A 268 " model vdw 2.192 3.040 nonbonded pdb=" O GLY C 141 " pdb=" OG SER C 194 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU A 145 " pdb=" OH TYR A 443 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.257 3.040 nonbonded pdb=" O MET A 744 " pdb=" OG1 THR A 748 " model vdw 2.263 3.040 ... (remaining 178960 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 46 through 656 or (resid 657 and (name N or name CA or nam \ e C or name O or name CB )) or resid 658 through 704 or (resid 705 and (name N o \ r name CA or name C or name O or name CB )) or resid 706 through 763 or (resid 7 \ 64 through 765 and (name N or name CA or name C or name O or name CB )) or resid \ 766 through 962 or resid 989 through 1011)) selection = (chain 'B' and (resid 46 through 541 or (resid 542 through 544 and (name N or na \ me CA or name C or name O or name CB )) or resid 545 through 1011)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.910 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.011 0.093 22741 Z= 0.515 Angle : 1.266 12.302 30826 Z= 0.680 Chirality : 0.067 0.294 3376 Planarity : 0.010 0.092 3965 Dihedral : 11.298 87.865 8423 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.13), residues: 2763 helix: -2.86 (0.13), residues: 810 sheet: -2.09 (0.17), residues: 701 loop : -2.63 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 164 TYR 0.047 0.005 TYR A 454 PHE 0.033 0.005 PHE A 288 TRP 0.048 0.005 TRP B 199 HIS 0.022 0.005 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.01129 (22731) covalent geometry : angle 1.26295 (30806) SS BOND : bond 0.00876 ( 10) SS BOND : angle 3.58869 ( 20) hydrogen bonds : bond 0.21656 ( 927) hydrogen bonds : angle 9.59949 ( 2724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 MET cc_start: 0.8916 (tpp) cc_final: 0.8689 (tpt) REVERT: A 577 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 870 MET cc_start: 0.8698 (mmm) cc_final: 0.8384 (mmm) REVERT: B 67 LEU cc_start: 0.8468 (pp) cc_final: 0.8001 (mp) REVERT: B 116 LEU cc_start: 0.7982 (mt) cc_final: 0.7654 (tp) REVERT: B 390 ILE cc_start: 0.9365 (mt) cc_final: 0.9145 (mt) REVERT: B 466 MET cc_start: 0.8981 (tmm) cc_final: 0.8730 (tmm) REVERT: B 511 LYS cc_start: 0.9212 (mttm) cc_final: 0.8739 (mtmt) REVERT: D 187 TYR cc_start: 0.8602 (t80) cc_final: 0.8360 (t80) REVERT: E 112 TRP cc_start: 0.8213 (m100) cc_final: 0.7678 (m100) REVERT: E 156 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7729 (pp20) REVERT: F 3 ILE cc_start: 0.8085 (mt) cc_final: 0.7869 (mt) REVERT: F 162 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7773 (mp0) REVERT: F 188 GLU cc_start: 0.8841 (pt0) cc_final: 0.8590 (mp0) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.1968 time to fit residues: 108.0853 Evaluate side-chains 149 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 134 HIS A 157 HIS A 167 GLN A 245 HIS A 407 GLN A 563 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 724 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN D 125 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 90 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.064187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.049805 restraints weight = 112391.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.051520 restraints weight = 51966.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052605 restraints weight = 30468.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.053366 restraints weight = 20933.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053804 restraints weight = 15978.104| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22741 Z= 0.156 Angle : 0.696 10.045 30826 Z= 0.365 Chirality : 0.046 0.329 3376 Planarity : 0.005 0.053 3965 Dihedral : 5.997 25.102 3013 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.72 % Allowed : 9.22 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.15), residues: 2763 helix: -0.87 (0.17), residues: 836 sheet: -1.27 (0.18), residues: 732 loop : -1.98 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 261 TYR 0.023 0.002 TYR C 57 PHE 0.024 0.002 PHE E 174 TRP 0.020 0.001 TRP B 495 HIS 0.009 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00329 (22731) covalent geometry : angle 0.69482 (30806) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.58476 ( 20) hydrogen bonds : bond 0.04562 ( 927) hydrogen bonds : angle 6.40202 ( 2724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8780 (mmm) cc_final: 0.8354 (mmm) REVERT: A 389 ASP cc_start: 0.9308 (t0) cc_final: 0.9069 (t0) REVERT: A 466 MET cc_start: 0.8891 (tmm) cc_final: 0.8639 (tpp) REVERT: A 556 MET cc_start: 0.8827 (tpp) cc_final: 0.8277 (tpt) REVERT: A 577 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 706 ASP cc_start: 0.7933 (m-30) cc_final: 0.7697 (m-30) REVERT: A 742 MET cc_start: 0.9178 (tpp) cc_final: 0.8775 (tpp) REVERT: A 870 MET cc_start: 0.9401 (mmm) cc_final: 0.8892 (mmm) REVERT: A 1000 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.7715 (mmm-85) REVERT: B 116 LEU cc_start: 0.7902 (mt) cc_final: 0.7561 (tp) REVERT: B 176 GLU cc_start: 0.9215 (mp0) cc_final: 0.8533 (tt0) REVERT: B 239 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8898 (mm-40) REVERT: B 332 HIS cc_start: 0.8437 (m170) cc_final: 0.7424 (t-90) REVERT: B 466 MET cc_start: 0.9301 (tmm) cc_final: 0.9081 (tmm) REVERT: B 511 LYS cc_start: 0.9197 (mttm) cc_final: 0.8832 (mtpt) REVERT: B 588 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8892 (tt) REVERT: B 592 MET cc_start: 0.8324 (mtt) cc_final: 0.7977 (mtt) REVERT: B 667 MET cc_start: 0.8920 (tpp) cc_final: 0.8706 (tpp) REVERT: B 690 MET cc_start: 0.8687 (mmp) cc_final: 0.7634 (mmp) REVERT: B 725 ILE cc_start: 0.8620 (mp) cc_final: 0.8216 (mt) REVERT: B 726 GLU cc_start: 0.8804 (tt0) cc_final: 0.8376 (tp30) REVERT: B 798 ASP cc_start: 0.7900 (t0) cc_final: 0.7479 (m-30) REVERT: B 806 MET cc_start: 0.9214 (mmm) cc_final: 0.8981 (mmm) REVERT: C 86 MET cc_start: 0.9386 (mmm) cc_final: 0.9046 (mmm) REVERT: C 114 GLN cc_start: 0.8130 (mp10) cc_final: 0.7922 (pm20) REVERT: E 112 TRP cc_start: 0.7622 (m100) cc_final: 0.7316 (m100) REVERT: E 214 LYS cc_start: 0.7272 (mtpt) cc_final: 0.7021 (mmtt) REVERT: F 99 PHE cc_start: 0.7615 (m-80) cc_final: 0.7341 (m-10) REVERT: F 162 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7709 (mp0) REVERT: F 188 GLU cc_start: 0.8873 (pt0) cc_final: 0.8606 (mp0) outliers start: 42 outliers final: 11 residues processed: 237 average time/residue: 0.1663 time to fit residues: 61.7940 Evaluate side-chains 160 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain c residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 208 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 206 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 205 optimal weight: 0.3980 chunk 126 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 203 optimal weight: 0.0170 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.064456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050164 restraints weight = 113000.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051909 restraints weight = 51518.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053045 restraints weight = 29931.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053748 restraints weight = 20301.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054244 restraints weight = 15560.526| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22741 Z= 0.123 Angle : 0.619 11.952 30826 Z= 0.319 Chirality : 0.044 0.308 3376 Planarity : 0.004 0.044 3965 Dihedral : 5.381 23.153 3013 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.76 % Allowed : 10.98 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.16), residues: 2763 helix: 0.10 (0.18), residues: 826 sheet: -0.93 (0.19), residues: 734 loop : -1.76 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 143 TYR 0.020 0.001 TYR C 57 PHE 0.020 0.001 PHE B 174 TRP 0.009 0.001 TRP C 50 HIS 0.005 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00266 (22731) covalent geometry : angle 0.61832 (30806) SS BOND : bond 0.00276 ( 10) SS BOND : angle 1.02652 ( 20) hydrogen bonds : bond 0.03864 ( 927) hydrogen bonds : angle 5.66389 ( 2724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8749 (mmm) cc_final: 0.8527 (mmm) REVERT: A 389 ASP cc_start: 0.9280 (t0) cc_final: 0.9054 (t0) REVERT: A 466 MET cc_start: 0.8926 (tmm) cc_final: 0.8636 (tpp) REVERT: A 556 MET cc_start: 0.8958 (tpp) cc_final: 0.8371 (tpt) REVERT: A 577 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 706 ASP cc_start: 0.7973 (m-30) cc_final: 0.7695 (m-30) REVERT: A 870 MET cc_start: 0.9346 (mmm) cc_final: 0.8844 (mmm) REVERT: A 996 THR cc_start: 0.9269 (m) cc_final: 0.9001 (p) REVERT: A 1000 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7810 (mmm-85) REVERT: B 116 LEU cc_start: 0.8019 (mt) cc_final: 0.7596 (tp) REVERT: B 156 GLU cc_start: 0.8398 (pm20) cc_final: 0.8195 (tm-30) REVERT: B 176 GLU cc_start: 0.9181 (mp0) cc_final: 0.8534 (tt0) REVERT: B 239 GLN cc_start: 0.9298 (mm-40) cc_final: 0.8866 (mm-40) REVERT: B 332 HIS cc_start: 0.8428 (m170) cc_final: 0.7819 (t70) REVERT: B 466 MET cc_start: 0.9311 (tmm) cc_final: 0.9018 (tmm) REVERT: B 511 LYS cc_start: 0.9157 (mttm) cc_final: 0.8774 (mtpt) REVERT: B 592 MET cc_start: 0.8396 (mtt) cc_final: 0.7976 (mtt) REVERT: B 667 MET cc_start: 0.8987 (tpp) cc_final: 0.8663 (tpp) REVERT: B 725 ILE cc_start: 0.8551 (mp) cc_final: 0.8194 (mt) REVERT: B 726 GLU cc_start: 0.8797 (tt0) cc_final: 0.8336 (tp30) REVERT: B 798 ASP cc_start: 0.7900 (t0) cc_final: 0.7449 (m-30) REVERT: B 817 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: C 86 MET cc_start: 0.9328 (mmm) cc_final: 0.9066 (mmm) REVERT: C 152 ASP cc_start: 0.8796 (p0) cc_final: 0.8436 (p0) REVERT: E 112 TRP cc_start: 0.7546 (m100) cc_final: 0.6944 (m100) REVERT: E 114 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: E 214 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6885 (mmtt) REVERT: F 162 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7648 (mp0) outliers start: 43 outliers final: 15 residues processed: 219 average time/residue: 0.1568 time to fit residues: 54.4321 Evaluate side-chains 167 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain c residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 172 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 132 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN B 762 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN E 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.061879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.047615 restraints weight = 115082.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049243 restraints weight = 53062.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050321 restraints weight = 31123.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050987 restraints weight = 21415.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.051442 restraints weight = 16517.067| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22741 Z= 0.225 Angle : 0.669 9.460 30826 Z= 0.345 Chirality : 0.044 0.210 3376 Planarity : 0.004 0.041 3965 Dihedral : 5.317 23.749 3013 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.09 % Allowed : 11.92 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.16), residues: 2763 helix: 0.48 (0.18), residues: 831 sheet: -0.77 (0.19), residues: 726 loop : -1.70 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 109 TYR 0.018 0.002 TYR C 57 PHE 0.022 0.002 PHE B 579 TRP 0.036 0.002 TRP D 149 HIS 0.007 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00488 (22731) covalent geometry : angle 0.66839 (30806) SS BOND : bond 0.00205 ( 10) SS BOND : angle 1.05232 ( 20) hydrogen bonds : bond 0.03845 ( 927) hydrogen bonds : angle 5.54449 ( 2724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.9283 (t0) cc_final: 0.9076 (t0) REVERT: A 466 MET cc_start: 0.8957 (tmm) cc_final: 0.8675 (tpp) REVERT: A 556 MET cc_start: 0.9108 (tpp) cc_final: 0.8534 (tpt) REVERT: A 577 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 706 ASP cc_start: 0.8011 (m-30) cc_final: 0.7735 (m-30) REVERT: A 742 MET cc_start: 0.9302 (tpp) cc_final: 0.8810 (tpp) REVERT: A 870 MET cc_start: 0.9414 (mmm) cc_final: 0.8897 (mmm) REVERT: A 877 MET cc_start: 0.8184 (ttt) cc_final: 0.7928 (ttt) REVERT: A 1000 ARG cc_start: 0.8361 (tpp-160) cc_final: 0.7889 (mmm-85) REVERT: B 116 LEU cc_start: 0.8159 (mt) cc_final: 0.7667 (tp) REVERT: B 239 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8874 (mm-40) REVERT: B 378 ASP cc_start: 0.8388 (t0) cc_final: 0.8091 (p0) REVERT: B 466 MET cc_start: 0.9319 (tmm) cc_final: 0.9033 (tmm) REVERT: B 511 LYS cc_start: 0.9193 (mttm) cc_final: 0.8863 (mtpt) REVERT: B 592 MET cc_start: 0.8416 (mtt) cc_final: 0.7707 (mtm) REVERT: B 667 MET cc_start: 0.9053 (tpp) cc_final: 0.8753 (tpp) REVERT: B 725 ILE cc_start: 0.8445 (mp) cc_final: 0.8163 (mt) REVERT: B 726 GLU cc_start: 0.8810 (tt0) cc_final: 0.8355 (tp30) REVERT: B 742 MET cc_start: 0.9124 (tpp) cc_final: 0.8923 (tpp) REVERT: B 798 ASP cc_start: 0.7786 (t0) cc_final: 0.7514 (m-30) REVERT: B 817 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: C 86 MET cc_start: 0.9416 (mmm) cc_final: 0.9173 (mmm) REVERT: E 112 TRP cc_start: 0.7638 (m100) cc_final: 0.7099 (m100) REVERT: E 114 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7875 (tp-100) REVERT: E 214 LYS cc_start: 0.7274 (mtpt) cc_final: 0.6946 (mmtt) REVERT: F 162 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7533 (mp0) REVERT: F 188 GLU cc_start: 0.8539 (pm20) cc_final: 0.7742 (mm-30) outliers start: 51 outliers final: 30 residues processed: 188 average time/residue: 0.1576 time to fit residues: 47.8507 Evaluate side-chains 161 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain c residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 5 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 234 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.062773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.048494 restraints weight = 112353.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050178 restraints weight = 51362.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051256 restraints weight = 29997.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051949 restraints weight = 20539.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052397 restraints weight = 15762.694| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22741 Z= 0.140 Angle : 0.601 8.027 30826 Z= 0.307 Chirality : 0.043 0.234 3376 Planarity : 0.004 0.044 3965 Dihedral : 5.098 23.550 3013 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.84 % Allowed : 12.58 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2763 helix: 0.75 (0.18), residues: 831 sheet: -0.69 (0.19), residues: 739 loop : -1.58 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 109 TYR 0.019 0.001 TYR B 547 PHE 0.022 0.001 PHE B 579 TRP 0.019 0.001 TRP D 149 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00307 (22731) covalent geometry : angle 0.60064 (30806) SS BOND : bond 0.00242 ( 10) SS BOND : angle 0.90035 ( 20) hydrogen bonds : bond 0.03509 ( 927) hydrogen bonds : angle 5.23279 ( 2724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.9278 (t0) cc_final: 0.9061 (t0) REVERT: A 466 MET cc_start: 0.8982 (tmm) cc_final: 0.8668 (tpp) REVERT: A 556 MET cc_start: 0.9088 (tpp) cc_final: 0.8515 (tpt) REVERT: A 577 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 592 MET cc_start: 0.8772 (mmm) cc_final: 0.8379 (mmm) REVERT: A 706 ASP cc_start: 0.8018 (m-30) cc_final: 0.7740 (m-30) REVERT: A 742 MET cc_start: 0.9244 (tpp) cc_final: 0.8721 (tpp) REVERT: A 870 MET cc_start: 0.9384 (mmm) cc_final: 0.8865 (mmm) REVERT: A 1000 ARG cc_start: 0.8361 (tpp-160) cc_final: 0.7823 (mmm-85) REVERT: B 116 LEU cc_start: 0.8147 (mt) cc_final: 0.7665 (tp) REVERT: B 176 GLU cc_start: 0.9150 (mp0) cc_final: 0.8552 (tm-30) REVERT: B 239 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8809 (mm-40) REVERT: B 378 ASP cc_start: 0.8360 (t0) cc_final: 0.8098 (p0) REVERT: B 466 MET cc_start: 0.9307 (tmm) cc_final: 0.9031 (tmm) REVERT: B 511 LYS cc_start: 0.9138 (mttm) cc_final: 0.8855 (mtmt) REVERT: B 521 LYS cc_start: 0.8365 (mptt) cc_final: 0.8090 (tptt) REVERT: B 592 MET cc_start: 0.8393 (mtt) cc_final: 0.7670 (mtm) REVERT: B 599 LEU cc_start: 0.9360 (mt) cc_final: 0.9145 (mt) REVERT: B 667 MET cc_start: 0.9102 (tpp) cc_final: 0.8788 (tpp) REVERT: B 725 ILE cc_start: 0.8439 (mp) cc_final: 0.8120 (mt) REVERT: B 726 GLU cc_start: 0.8759 (tt0) cc_final: 0.8325 (tp30) REVERT: B 742 MET cc_start: 0.9104 (tpp) cc_final: 0.8851 (tpp) REVERT: B 798 ASP cc_start: 0.7763 (t0) cc_final: 0.7532 (m-30) REVERT: C 86 MET cc_start: 0.9402 (mmm) cc_final: 0.9160 (mmm) REVERT: D 5 MET cc_start: 0.7953 (tpp) cc_final: 0.7668 (mmm) REVERT: E 86 MET cc_start: 0.7665 (mpp) cc_final: 0.7385 (mpp) REVERT: E 114 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: E 214 LYS cc_start: 0.7255 (mtpt) cc_final: 0.6940 (mmtt) REVERT: F 162 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7551 (mp0) REVERT: F 188 GLU cc_start: 0.8583 (pm20) cc_final: 0.7915 (mm-30) outliers start: 45 outliers final: 28 residues processed: 186 average time/residue: 0.1465 time to fit residues: 44.2676 Evaluate side-chains 164 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 17 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 162 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045660 restraints weight = 117563.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047209 restraints weight = 54642.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.048209 restraints weight = 32353.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.048868 restraints weight = 22327.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049270 restraints weight = 17304.361| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22741 Z= 0.320 Angle : 0.780 12.142 30826 Z= 0.397 Chirality : 0.047 0.320 3376 Planarity : 0.005 0.050 3965 Dihedral : 5.589 24.507 3013 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.29 % Allowed : 12.90 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2763 helix: 0.33 (0.17), residues: 853 sheet: -0.91 (0.18), residues: 761 loop : -1.56 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 838 TYR 0.022 0.002 TYR A 433 PHE 0.032 0.003 PHE B 174 TRP 0.024 0.002 TRP D 149 HIS 0.009 0.002 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00688 (22731) covalent geometry : angle 0.78003 (30806) SS BOND : bond 0.00354 ( 10) SS BOND : angle 1.20320 ( 20) hydrogen bonds : bond 0.04189 ( 927) hydrogen bonds : angle 5.69069 ( 2724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9101 (mmm) cc_final: 0.8783 (mmt) REVERT: A 466 MET cc_start: 0.8976 (tmm) cc_final: 0.8668 (tpp) REVERT: A 556 MET cc_start: 0.9157 (tpp) cc_final: 0.8709 (tpt) REVERT: A 577 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 592 MET cc_start: 0.8878 (mmm) cc_final: 0.8601 (mmm) REVERT: A 706 ASP cc_start: 0.7967 (m-30) cc_final: 0.7740 (m-30) REVERT: A 742 MET cc_start: 0.9267 (tpp) cc_final: 0.8792 (tpp) REVERT: A 870 MET cc_start: 0.9423 (mmm) cc_final: 0.8870 (mmm) REVERT: A 877 MET cc_start: 0.8036 (ttt) cc_final: 0.7818 (tmt) REVERT: B 242 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9320 (pp) REVERT: B 466 MET cc_start: 0.9328 (tmm) cc_final: 0.9014 (tmm) REVERT: B 556 MET cc_start: 0.8603 (tpp) cc_final: 0.8250 (tpp) REVERT: B 592 MET cc_start: 0.8532 (mtt) cc_final: 0.7835 (mtm) REVERT: B 599 LEU cc_start: 0.9364 (mt) cc_final: 0.9145 (mt) REVERT: B 625 TYR cc_start: 0.8553 (m-10) cc_final: 0.8245 (m-80) REVERT: B 667 MET cc_start: 0.9106 (tpp) cc_final: 0.8809 (tpp) REVERT: B 725 ILE cc_start: 0.8702 (mp) cc_final: 0.8287 (mt) REVERT: B 726 GLU cc_start: 0.8793 (tt0) cc_final: 0.8309 (tp30) REVERT: B 742 MET cc_start: 0.9098 (tpp) cc_final: 0.8833 (tpp) REVERT: B 894 LEU cc_start: 0.9602 (tt) cc_final: 0.9292 (pp) REVERT: D 5 MET cc_start: 0.7870 (tpp) cc_final: 0.7636 (mmm) REVERT: E 46 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7885 (ptpp) REVERT: E 86 MET cc_start: 0.7747 (mpp) cc_final: 0.7396 (mpp) REVERT: E 114 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8255 (tp-100) REVERT: E 214 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6889 (mmtt) REVERT: F 162 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7363 (mp0) outliers start: 56 outliers final: 41 residues processed: 174 average time/residue: 0.1441 time to fit residues: 41.5312 Evaluate side-chains 162 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 236 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 261 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 294 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.061313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047125 restraints weight = 114057.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048748 restraints weight = 52517.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.049809 restraints weight = 30806.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.050471 restraints weight = 21104.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.050920 restraints weight = 16253.237| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22741 Z= 0.163 Angle : 0.635 13.220 30826 Z= 0.321 Chirality : 0.044 0.278 3376 Planarity : 0.004 0.045 3965 Dihedral : 5.237 22.174 3013 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.01 % Allowed : 13.60 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.16), residues: 2763 helix: 0.66 (0.18), residues: 848 sheet: -0.69 (0.19), residues: 746 loop : -1.46 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 143 TYR 0.017 0.001 TYR c 14 PHE 0.028 0.001 PHE B 174 TRP 0.021 0.001 TRP D 149 HIS 0.005 0.001 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00356 (22731) covalent geometry : angle 0.63446 (30806) SS BOND : bond 0.00272 ( 10) SS BOND : angle 0.92985 ( 20) hydrogen bonds : bond 0.03559 ( 927) hydrogen bonds : angle 5.26815 ( 2724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9089 (mmm) cc_final: 0.8734 (mmm) REVERT: A 389 ASP cc_start: 0.9268 (t0) cc_final: 0.9050 (t0) REVERT: A 466 MET cc_start: 0.9005 (tmm) cc_final: 0.8648 (tpp) REVERT: A 556 MET cc_start: 0.9123 (tpp) cc_final: 0.8564 (tpt) REVERT: A 577 GLU cc_start: 0.8595 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 592 MET cc_start: 0.8805 (mmm) cc_final: 0.8409 (mmm) REVERT: A 706 ASP cc_start: 0.7973 (m-30) cc_final: 0.7744 (m-30) REVERT: A 742 MET cc_start: 0.9256 (tpp) cc_final: 0.8754 (tpp) REVERT: A 788 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8784 (t0) REVERT: A 870 MET cc_start: 0.9389 (mmm) cc_final: 0.8843 (mmm) REVERT: A 877 MET cc_start: 0.8023 (ttt) cc_final: 0.7823 (tmt) REVERT: B 176 GLU cc_start: 0.9137 (mp0) cc_final: 0.8607 (pp20) REVERT: B 242 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9292 (pp) REVERT: B 282 ASN cc_start: 0.8796 (m-40) cc_final: 0.8074 (p0) REVERT: B 332 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8090 (t70) REVERT: B 466 MET cc_start: 0.9333 (tmm) cc_final: 0.9041 (tmm) REVERT: B 511 LYS cc_start: 0.9207 (mttm) cc_final: 0.8845 (mtpt) REVERT: B 592 MET cc_start: 0.8500 (mtt) cc_final: 0.7928 (mtt) REVERT: B 599 LEU cc_start: 0.9374 (mt) cc_final: 0.9165 (mt) REVERT: B 667 MET cc_start: 0.9065 (tpp) cc_final: 0.8737 (tpp) REVERT: B 725 ILE cc_start: 0.8530 (mp) cc_final: 0.8156 (mt) REVERT: B 726 GLU cc_start: 0.8784 (tt0) cc_final: 0.8327 (tp30) REVERT: B 742 MET cc_start: 0.9066 (tpp) cc_final: 0.8814 (tpp) REVERT: B 894 LEU cc_start: 0.9585 (tt) cc_final: 0.9282 (pp) REVERT: B 943 MET cc_start: 0.7512 (mmp) cc_final: 0.7181 (mmp) REVERT: C 86 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9160 (tpp) REVERT: D 5 MET cc_start: 0.7881 (tpp) cc_final: 0.7677 (mmm) REVERT: E 86 MET cc_start: 0.7641 (mpp) cc_final: 0.7356 (mpp) REVERT: E 114 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: E 214 LYS cc_start: 0.7123 (mtpt) cc_final: 0.6840 (mmtt) REVERT: F 162 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7288 (mp0) REVERT: F 188 GLU cc_start: 0.8071 (pm20) cc_final: 0.7478 (mm-30) outliers start: 49 outliers final: 35 residues processed: 174 average time/residue: 0.1372 time to fit residues: 40.0470 Evaluate side-chains 163 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 131 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 88 optimal weight: 0.0570 chunk 224 optimal weight: 0.0040 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN E 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.062873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048579 restraints weight = 112540.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050258 restraints weight = 51648.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.051348 restraints weight = 30190.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052037 restraints weight = 20665.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052492 restraints weight = 15887.452| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22741 Z= 0.107 Angle : 0.599 11.603 30826 Z= 0.300 Chirality : 0.043 0.214 3376 Planarity : 0.004 0.048 3965 Dihedral : 4.910 21.379 3013 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.88 % Allowed : 14.17 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2763 helix: 1.08 (0.18), residues: 829 sheet: -0.52 (0.19), residues: 747 loop : -1.37 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 143 TYR 0.016 0.001 TYR c 14 PHE 0.028 0.001 PHE B 174 TRP 0.018 0.001 TRP D 149 HIS 0.005 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00235 (22731) covalent geometry : angle 0.59889 (30806) SS BOND : bond 0.00222 ( 10) SS BOND : angle 0.81357 ( 20) hydrogen bonds : bond 0.03227 ( 927) hydrogen bonds : angle 4.96079 ( 2724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9032 (mmm) cc_final: 0.8818 (mmt) REVERT: A 389 ASP cc_start: 0.9248 (t0) cc_final: 0.9014 (t0) REVERT: A 466 MET cc_start: 0.9052 (tmm) cc_final: 0.8677 (tpp) REVERT: A 556 MET cc_start: 0.9129 (tpp) cc_final: 0.8548 (tpt) REVERT: A 577 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 592 MET cc_start: 0.8801 (mmm) cc_final: 0.8410 (mmm) REVERT: A 706 ASP cc_start: 0.7987 (m-30) cc_final: 0.7736 (m-30) REVERT: A 742 MET cc_start: 0.9207 (tpp) cc_final: 0.8671 (tpp) REVERT: A 870 MET cc_start: 0.9398 (mmm) cc_final: 0.8873 (mmm) REVERT: B 176 GLU cc_start: 0.9108 (mp0) cc_final: 0.8557 (pp20) REVERT: B 332 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.8001 (t-90) REVERT: B 334 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 466 MET cc_start: 0.9318 (tmm) cc_final: 0.9037 (tmm) REVERT: B 511 LYS cc_start: 0.9209 (mttm) cc_final: 0.8984 (mmtp) REVERT: B 599 LEU cc_start: 0.9389 (mt) cc_final: 0.9186 (mt) REVERT: B 667 MET cc_start: 0.9052 (tpp) cc_final: 0.8735 (tpp) REVERT: B 725 ILE cc_start: 0.8578 (mp) cc_final: 0.8289 (mt) REVERT: B 726 GLU cc_start: 0.8818 (tt0) cc_final: 0.8368 (tp30) REVERT: B 742 MET cc_start: 0.9066 (tpp) cc_final: 0.8829 (tpp) REVERT: B 860 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 894 LEU cc_start: 0.9566 (tt) cc_final: 0.9258 (pp) REVERT: B 943 MET cc_start: 0.7423 (mmp) cc_final: 0.7180 (mmp) REVERT: C 86 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8786 (mmm) REVERT: C 125 LYS cc_start: 0.8773 (tptp) cc_final: 0.8530 (tptp) REVERT: E 86 MET cc_start: 0.7594 (mpp) cc_final: 0.7386 (mpp) REVERT: E 112 TRP cc_start: 0.7664 (m100) cc_final: 0.7038 (m100) REVERT: E 114 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: E 214 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6856 (mmtt) REVERT: F 162 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7207 (mp0) outliers start: 46 outliers final: 30 residues processed: 181 average time/residue: 0.1502 time to fit residues: 44.6951 Evaluate side-chains 163 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 294 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS B 841 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.059681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045596 restraints weight = 117231.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047154 restraints weight = 54497.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048167 restraints weight = 32217.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048823 restraints weight = 22259.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049258 restraints weight = 17219.714| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22741 Z= 0.328 Angle : 0.780 12.793 30826 Z= 0.393 Chirality : 0.047 0.274 3376 Planarity : 0.005 0.052 3965 Dihedral : 5.390 24.755 3013 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.01 % Allowed : 14.30 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2763 helix: 0.53 (0.18), residues: 856 sheet: -0.77 (0.18), residues: 781 loop : -1.36 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 838 TYR 0.020 0.002 TYR A 433 PHE 0.028 0.002 PHE B 174 TRP 0.019 0.002 TRP D 149 HIS 0.010 0.002 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00702 (22731) covalent geometry : angle 0.77981 (30806) SS BOND : bond 0.00497 ( 10) SS BOND : angle 1.12306 ( 20) hydrogen bonds : bond 0.04042 ( 927) hydrogen bonds : angle 5.52647 ( 2724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9043 (mmm) cc_final: 0.8780 (mmm) REVERT: A 466 MET cc_start: 0.8990 (tmm) cc_final: 0.8631 (tpp) REVERT: A 556 MET cc_start: 0.9146 (tpp) cc_final: 0.8630 (tpt) REVERT: A 577 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 592 MET cc_start: 0.8879 (mmm) cc_final: 0.8565 (mmm) REVERT: A 667 MET cc_start: 0.8768 (tmm) cc_final: 0.8480 (tmm) REVERT: A 706 ASP cc_start: 0.7973 (m-30) cc_final: 0.7757 (m-30) REVERT: A 742 MET cc_start: 0.9279 (tpp) cc_final: 0.8793 (tpp) REVERT: A 870 MET cc_start: 0.9439 (mmm) cc_final: 0.8859 (mmm) REVERT: A 877 MET cc_start: 0.8064 (ttt) cc_final: 0.7734 (tmt) REVERT: B 176 GLU cc_start: 0.9046 (mp0) cc_final: 0.8613 (pp20) REVERT: B 332 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (t70) REVERT: B 466 MET cc_start: 0.9333 (tmm) cc_final: 0.9013 (tmm) REVERT: B 599 LEU cc_start: 0.9381 (mt) cc_final: 0.9072 (mt) REVERT: B 667 MET cc_start: 0.9104 (tpp) cc_final: 0.8771 (tpp) REVERT: B 725 ILE cc_start: 0.8717 (mp) cc_final: 0.8349 (mt) REVERT: B 726 GLU cc_start: 0.8814 (tt0) cc_final: 0.8405 (tp30) REVERT: B 742 MET cc_start: 0.9088 (tpp) cc_final: 0.8840 (tpp) REVERT: B 894 LEU cc_start: 0.9586 (tt) cc_final: 0.9273 (pp) REVERT: B 943 MET cc_start: 0.7682 (mmp) cc_final: 0.7417 (mmp) REVERT: C 86 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.9086 (tpp) REVERT: E 114 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8187 (tp-100) REVERT: E 214 LYS cc_start: 0.7148 (mtpt) cc_final: 0.6829 (mmtt) REVERT: F 162 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7211 (mp0) outliers start: 49 outliers final: 36 residues processed: 156 average time/residue: 0.1385 time to fit residues: 36.4805 Evaluate side-chains 151 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 841 ASN Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 87 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 224 optimal weight: 0.0470 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 217 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.062026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047819 restraints weight = 113913.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049489 restraints weight = 52011.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050558 restraints weight = 30435.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051259 restraints weight = 20800.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051679 restraints weight = 15931.562| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22741 Z= 0.117 Angle : 0.637 16.749 30826 Z= 0.315 Chirality : 0.044 0.208 3376 Planarity : 0.004 0.047 3965 Dihedral : 5.031 23.385 3013 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.68 % Allowed : 14.79 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2763 helix: 0.97 (0.18), residues: 834 sheet: -0.54 (0.19), residues: 767 loop : -1.27 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 838 TYR 0.016 0.001 TYR c 14 PHE 0.028 0.001 PHE B 174 TRP 0.017 0.001 TRP D 149 HIS 0.005 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00266 (22731) covalent geometry : angle 0.63705 (30806) SS BOND : bond 0.00239 ( 10) SS BOND : angle 0.79999 ( 20) hydrogen bonds : bond 0.03381 ( 927) hydrogen bonds : angle 5.04552 ( 2724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.9032 (tmm) cc_final: 0.8652 (tpp) REVERT: A 556 MET cc_start: 0.9128 (tpp) cc_final: 0.8562 (tpt) REVERT: A 577 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 592 MET cc_start: 0.8830 (mmm) cc_final: 0.8411 (mmm) REVERT: A 667 MET cc_start: 0.8722 (tmm) cc_final: 0.8480 (tmm) REVERT: A 706 ASP cc_start: 0.7889 (m-30) cc_final: 0.7657 (m-30) REVERT: A 742 MET cc_start: 0.9239 (tpp) cc_final: 0.8733 (tpp) REVERT: A 744 MET cc_start: 0.9195 (tmm) cc_final: 0.8890 (tmm) REVERT: A 870 MET cc_start: 0.9390 (mmm) cc_final: 0.8834 (mmm) REVERT: A 877 MET cc_start: 0.8005 (ttt) cc_final: 0.7775 (tmt) REVERT: B 176 GLU cc_start: 0.9079 (mp0) cc_final: 0.8556 (pp20) REVERT: B 282 ASN cc_start: 0.8803 (m-40) cc_final: 0.8124 (p0) REVERT: B 332 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8115 (t70) REVERT: B 466 MET cc_start: 0.9302 (tmm) cc_final: 0.9016 (tmm) REVERT: B 559 LEU cc_start: 0.8641 (tt) cc_final: 0.8424 (tt) REVERT: B 599 LEU cc_start: 0.9380 (mt) cc_final: 0.9175 (mt) REVERT: B 667 MET cc_start: 0.9058 (tpp) cc_final: 0.8713 (tpp) REVERT: B 725 ILE cc_start: 0.8635 (mp) cc_final: 0.8360 (mt) REVERT: B 726 GLU cc_start: 0.8826 (tt0) cc_final: 0.8376 (tp30) REVERT: B 894 LEU cc_start: 0.9522 (tt) cc_final: 0.9226 (pp) REVERT: B 943 MET cc_start: 0.7384 (mmp) cc_final: 0.7157 (mmp) REVERT: C 86 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8861 (mmm) REVERT: C 125 LYS cc_start: 0.9083 (tppt) cc_final: 0.8782 (ttmm) REVERT: E 86 MET cc_start: 0.8299 (mpp) cc_final: 0.8052 (mpp) REVERT: E 112 TRP cc_start: 0.7785 (m100) cc_final: 0.7199 (m100) REVERT: E 114 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8130 (tp-100) REVERT: E 214 LYS cc_start: 0.7024 (mtpt) cc_final: 0.6689 (mmtt) REVERT: F 162 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7207 (mp0) REVERT: F 188 GLU cc_start: 0.8192 (pm20) cc_final: 0.7626 (mm-30) REVERT: c 2 ILE cc_start: 0.8471 (pt) cc_final: 0.8151 (mp) outliers start: 41 outliers final: 34 residues processed: 166 average time/residue: 0.1461 time to fit residues: 40.4595 Evaluate side-chains 163 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 841 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.061489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.047288 restraints weight = 114535.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.048924 restraints weight = 52648.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049977 restraints weight = 30935.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.050643 restraints weight = 21192.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051112 restraints weight = 16324.350| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22741 Z= 0.164 Angle : 0.646 16.554 30826 Z= 0.320 Chirality : 0.044 0.190 3376 Planarity : 0.004 0.049 3965 Dihedral : 4.991 22.661 3013 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.64 % Allowed : 15.03 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2763 helix: 1.00 (0.18), residues: 835 sheet: -0.50 (0.19), residues: 769 loop : -1.23 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 143 TYR 0.013 0.001 TYR B 547 PHE 0.028 0.001 PHE B 174 TRP 0.013 0.001 TRP D 149 HIS 0.005 0.001 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00367 (22731) covalent geometry : angle 0.64570 (30806) SS BOND : bond 0.00257 ( 10) SS BOND : angle 0.89666 ( 20) hydrogen bonds : bond 0.03406 ( 927) hydrogen bonds : angle 5.07259 ( 2724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.87 seconds wall clock time: 72 minutes 50.59 seconds (4370.59 seconds total)