Starting phenix.real_space_refine on Sun Sep 29 10:24:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/09_2024/6b70_7062.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/09_2024/6b70_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/09_2024/6b70_7062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/09_2024/6b70_7062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/09_2024/6b70_7062.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b70_7062/09_2024/6b70_7062.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'ARG:plan': 1, 'ASP: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: 12.61, per 1000 atoms: 0.57 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: 5.34 Conformation dependent library (CDL) restraints added in 2.7 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: 3.07 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: 8.33 Time building geometry restraints manager: 6.31 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: 0.010 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.600 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.100 ------------------------------------------------------------------------------- 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 22731 Z= 0.729 Angle : 1.263 12.302 30806 Z= 0.679 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 : 6.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.048 0.005 TRP B 199 HIS 0.022 0.005 HIS B 157 PHE 0.033 0.005 PHE A 288 TYR 0.047 0.005 TYR A 454 ARG 0.017 0.002 ARG A 164 *********************** 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 fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.690 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: 0.8690 (tpt) REVERT: A 577 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 870 MET cc_start: 0.8698 (mmm) cc_final: 0.8383 (mmm) REVERT: B 67 LEU cc_start: 0.8468 (pp) cc_final: 0.8000 (mp) REVERT: B 116 LEU cc_start: 0.7982 (mt) cc_final: 0.7655 (tp) REVERT: B 390 ILE cc_start: 0.9365 (mt) cc_final: 0.9144 (mt) REVERT: B 466 MET cc_start: 0.8981 (tmm) cc_final: 0.8729 (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: 0.8305 (t80) REVERT: D 212 ARG cc_start: 0.5925 (mtm-85) cc_final: 0.5305 (ptm-80) 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: 0.8589 (mp0) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.4039 time to fit residues: 221.8045 Evaluate side-chains 150 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 249 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22731 Z= 0.195 Angle : 0.693 10.177 30806 Z= 0.363 Chirality : 0.046 0.319 3376 Planarity : 0.006 0.059 3965 Dihedral : 6.059 25.833 3013 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.72 % Allowed : 8.64 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2763 helix: -0.96 (0.17), residues: 833 sheet: -1.29 (0.18), residues: 734 loop : -2.02 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 495 HIS 0.009 0.001 HIS A 157 PHE 0.026 0.002 PHE E 174 TYR 0.024 0.002 TYR C 57 ARG 0.005 0.001 ARG B 261 *********************** 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 249 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 2.529 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 870 MET cc_start: 0.8541 (mmm) cc_final: 0.8286 (mmm) REVERT: B 116 LEU cc_start: 0.7977 (mt) cc_final: 0.7697 (tp) REVERT: B 239 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8566 (mm-40) REVERT: B 332 HIS cc_start: 0.8032 (m170) cc_final: 0.7647 (t-90) REVERT: B 341 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: B 414 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8864 (tm) REVERT: B 466 MET cc_start: 0.8921 (tmm) cc_final: 0.8712 (tmm) REVERT: B 588 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 690 MET cc_start: 0.8919 (mmp) cc_final: 0.7884 (mmp) REVERT: B 806 MET cc_start: 0.9127 (mmm) cc_final: 0.8918 (mmm) REVERT: E 73 ILE cc_start: 0.9180 (tt) cc_final: 0.8895 (tp) REVERT: E 130 PHE cc_start: 0.7223 (m-80) cc_final: 0.6985 (m-80) REVERT: E 214 LYS cc_start: 0.7219 (mtpt) cc_final: 0.6997 (mmtt) REVERT: F 99 PHE cc_start: 0.7515 (m-80) cc_final: 0.7234 (m-10) REVERT: F 106 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6651 (tp30) REVERT: F 188 GLU cc_start: 0.8828 (pt0) cc_final: 0.8563 (mp0) outliers start: 42 outliers final: 12 residues processed: 242 average time/residue: 0.3407 time to fit residues: 129.3941 Evaluate side-chains 165 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 414 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 33 SER Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 106 GLU 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 138 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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** B 323 GLN B 475 ASN B 762 GLN B 841 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22731 Z= 0.376 Angle : 0.751 11.208 30806 Z= 0.387 Chirality : 0.046 0.309 3376 Planarity : 0.005 0.053 3965 Dihedral : 5.780 25.372 3013 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.54 % Allowed : 10.98 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2763 helix: -0.07 (0.17), residues: 829 sheet: -1.12 (0.18), residues: 748 loop : -1.80 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 355 HIS 0.008 0.002 HIS A 885 PHE 0.024 0.002 PHE E 174 TYR 0.019 0.002 TYR B 547 ARG 0.009 0.001 ARG B 838 *********************** 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 204 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 142 time to evaluate : 2.576 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: A 592 MET cc_start: 0.7851 (mmm) cc_final: 0.7650 (mmm) REVERT: A 870 MET cc_start: 0.8570 (mmm) cc_final: 0.8294 (mmm) REVERT: B 116 LEU cc_start: 0.8297 (mt) cc_final: 0.7802 (tp) REVERT: B 243 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8981 (mtpp) REVERT: B 466 MET cc_start: 0.9015 (tmm) cc_final: 0.8662 (tmm) REVERT: B 511 LYS cc_start: 0.9166 (mttm) cc_final: 0.8851 (mtpt) REVERT: B 667 MET cc_start: 0.8124 (tpp) cc_final: 0.7908 (tpp) REVERT: B 817 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: B 894 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9102 (tt) REVERT: E 49 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7664 (mt-10) REVERT: E 73 ILE cc_start: 0.9240 (tt) cc_final: 0.8961 (tp) REVERT: E 86 MET cc_start: 0.8022 (mpp) cc_final: 0.7740 (mpp) REVERT: E 214 LYS cc_start: 0.6988 (mtpt) cc_final: 0.6776 (mmtt) REVERT: F 188 GLU cc_start: 0.8908 (pt0) cc_final: 0.8611 (mp0) outliers start: 62 outliers final: 27 residues processed: 195 average time/residue: 0.3334 time to fit residues: 103.8308 Evaluate side-chains 156 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 2.750 ------------------------------------------------------------------------------- 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 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 243 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 341 GLU 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 645 ILE Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 894 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 170 LYS Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 71 ASP 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 247 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 119 optimal weight: 0.3980 chunk 167 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 71 optimal weight: 0.0040 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22731 Z= 0.176 Angle : 0.605 9.732 30806 Z= 0.312 Chirality : 0.044 0.204 3376 Planarity : 0.004 0.048 3965 Dihedral : 5.280 23.202 3013 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.68 % Allowed : 11.80 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2763 helix: 0.55 (0.18), residues: 830 sheet: -0.87 (0.19), residues: 740 loop : -1.69 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 149 HIS 0.004 0.001 HIS B 134 PHE 0.022 0.001 PHE B 579 TYR 0.019 0.001 TYR C 57 ARG 0.009 0.000 ARG D 143 *********************** 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 201 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 2.798 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 870 MET cc_start: 0.8479 (mmm) cc_final: 0.8225 (mmm) REVERT: B 116 LEU cc_start: 0.8269 (mt) cc_final: 0.7793 (tp) REVERT: B 176 GLU cc_start: 0.8917 (mp0) cc_final: 0.8467 (tm-30) REVERT: B 239 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8477 (mm110) REVERT: B 334 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8355 (tp) REVERT: B 466 MET cc_start: 0.8960 (tmm) cc_final: 0.8661 (tmm) REVERT: B 511 LYS cc_start: 0.9048 (mttm) cc_final: 0.8813 (mtmt) REVERT: B 592 MET cc_start: 0.8078 (mtt) cc_final: 0.7806 (mtm) REVERT: D 5 MET cc_start: 0.8040 (mmm) cc_final: 0.7824 (tpp) REVERT: F 188 GLU cc_start: 0.8909 (pt0) cc_final: 0.8625 (mp0) outliers start: 41 outliers final: 23 residues processed: 195 average time/residue: 0.3129 time to fit residues: 99.3178 Evaluate side-chains 153 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 334 LEU Chi-restraints excluded: chain A residue 347 LEU 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 B residue 153 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 874 ILE 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 65 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 9 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.9524 ------------------------------------------------------------------------------- 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 762 GLN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22731 Z= 0.169 Angle : 0.597 14.721 30806 Z= 0.302 Chirality : 0.043 0.281 3376 Planarity : 0.004 0.045 3965 Dihedral : 5.025 23.813 3013 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.60 % Allowed : 12.90 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2763 helix: 0.87 (0.18), residues: 829 sheet: -0.71 (0.19), residues: 737 loop : -1.55 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 776 HIS 0.005 0.001 HIS E 102 PHE 0.030 0.001 PHE B 174 TYR 0.018 0.001 TYR C 57 ARG 0.005 0.000 ARG D 143 *********************** 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 187 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 2.828 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 870 MET cc_start: 0.8456 (mmm) cc_final: 0.8221 (mmm) REVERT: B 116 LEU cc_start: 0.8284 (mt) cc_final: 0.7774 (tp) REVERT: B 239 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8488 (mm-40) REVERT: B 334 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8419 (tp) REVERT: B 466 MET cc_start: 0.8980 (tmm) cc_final: 0.8726 (tmm) REVERT: B 511 LYS cc_start: 0.9045 (mttm) cc_final: 0.8822 (mtmt) REVERT: B 592 MET cc_start: 0.8032 (mtt) cc_final: 0.7632 (mtm) REVERT: F 71 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7340 (p0) REVERT: F 92 SER cc_start: 0.7564 (m) cc_final: 0.7302 (p) outliers start: 39 outliers final: 27 residues processed: 180 average time/residue: 0.3010 time to fit residues: 89.5226 Evaluate side-chains 161 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 334 LEU Chi-restraints excluded: chain A residue 347 LEU 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 860 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 345 SER 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 874 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 266 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22731 Z= 0.385 Angle : 0.739 11.025 30806 Z= 0.376 Chirality : 0.046 0.232 3376 Planarity : 0.005 0.049 3965 Dihedral : 5.402 24.276 3013 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.46 % Allowed : 12.41 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2763 helix: 0.55 (0.18), residues: 842 sheet: -0.81 (0.19), residues: 757 loop : -1.48 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 36 HIS 0.008 0.002 HIS B 393 PHE 0.032 0.002 PHE B 174 TYR 0.021 0.002 TYR A 433 ARG 0.007 0.001 ARG A 838 *********************** 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 fitting. rotamer outliers: 60 poor density : 124 time to evaluate : 2.811 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: A 870 MET cc_start: 0.8534 (mmm) cc_final: 0.8243 (mmm) REVERT: B 116 LEU cc_start: 0.8450 (mt) cc_final: 0.7848 (tp) REVERT: B 176 GLU cc_start: 0.8901 (mp0) cc_final: 0.8538 (pp20) REVERT: B 243 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9014 (mtpt) REVERT: B 466 MET cc_start: 0.9056 (tmm) cc_final: 0.8738 (tmm) REVERT: B 592 MET cc_start: 0.8079 (mtt) cc_final: 0.7695 (mtm) REVERT: C 149 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8085 (pp) REVERT: F 188 GLU cc_start: 0.8550 (pm20) cc_final: 0.7551 (mm-30) outliers start: 60 outliers final: 44 residues processed: 173 average time/residue: 0.3316 time to fit residues: 93.6631 Evaluate side-chains 163 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 117 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 946 VAL Chi-restraints excluded: chain A residue 963 MET 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 243 LYS 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 341 GLU 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 645 ILE Chi-restraints excluded: chain B residue 681 HIS 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 149 LEU 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 170 LYS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22731 Z= 0.191 Angle : 0.619 11.909 30806 Z= 0.311 Chirality : 0.043 0.260 3376 Planarity : 0.004 0.048 3965 Dihedral : 5.087 22.901 3013 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.68 % Allowed : 13.76 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2763 helix: 0.93 (0.18), residues: 828 sheet: -0.60 (0.19), residues: 733 loop : -1.45 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 50 HIS 0.004 0.001 HIS E 102 PHE 0.031 0.001 PHE B 174 TYR 0.016 0.001 TYR c 14 ARG 0.003 0.000 ARG D 143 *********************** 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 178 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 2.401 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 870 MET cc_start: 0.8454 (mmm) cc_final: 0.8197 (mmm) REVERT: B 116 LEU cc_start: 0.8381 (mt) cc_final: 0.7757 (tp) REVERT: C 149 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8031 (pp) REVERT: F 188 GLU cc_start: 0.8467 (pm20) cc_final: 0.7635 (mm-30) outliers start: 41 outliers final: 26 residues processed: 169 average time/residue: 0.3133 time to fit residues: 87.1629 Evaluate side-chains 151 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 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 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 341 GLU 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 149 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain c residue 3 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 208 optimal weight: 4.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 781 GLN ** 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 ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22731 Z= 0.371 Angle : 0.722 12.239 30806 Z= 0.363 Chirality : 0.045 0.270 3376 Planarity : 0.005 0.051 3965 Dihedral : 5.323 23.712 3013 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.17 % Allowed : 13.72 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2763 helix: 0.64 (0.18), residues: 850 sheet: -0.73 (0.19), residues: 769 loop : -1.36 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 36 HIS 0.008 0.002 HIS A 885 PHE 0.031 0.002 PHE B 174 TYR 0.020 0.002 TYR B 666 ARG 0.006 0.001 ARG A 838 *********************** 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 177 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 124 time to evaluate : 2.554 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 667 MET cc_start: 0.8296 (tmm) cc_final: 0.8059 (tmm) REVERT: A 870 MET cc_start: 0.8554 (mmm) cc_final: 0.8240 (mmm) REVERT: B 116 LEU cc_start: 0.8496 (mt) cc_final: 0.7829 (tp) REVERT: B 176 GLU cc_start: 0.8932 (mp0) cc_final: 0.8557 (pp20) REVERT: B 282 ASN cc_start: 0.8342 (m-40) cc_final: 0.7695 (p0) REVERT: B 592 MET cc_start: 0.8053 (mtt) cc_final: 0.7652 (mtm) REVERT: F 188 GLU cc_start: 0.8509 (pm20) cc_final: 0.7779 (mm-30) outliers start: 53 outliers final: 42 residues processed: 169 average time/residue: 0.3111 time to fit residues: 86.1914 Evaluate side-chains 159 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 2.444 ------------------------------------------------------------------------------- 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 946 VAL Chi-restraints excluded: chain A residue 963 MET 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 315 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 645 ILE 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 874 ILE Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 48 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 246 optimal weight: 30.0000 chunk 148 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 193 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22731 Z= 0.180 Angle : 0.644 14.542 30806 Z= 0.316 Chirality : 0.043 0.212 3376 Planarity : 0.004 0.047 3965 Dihedral : 5.034 23.508 3013 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.43 % Allowed : 14.50 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2763 helix: 0.94 (0.18), residues: 829 sheet: -0.58 (0.19), residues: 756 loop : -1.26 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 776 HIS 0.005 0.001 HIS E 102 PHE 0.029 0.001 PHE B 174 TYR 0.023 0.001 TYR B 666 ARG 0.007 0.000 ARG B 668 *********************** 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 168 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 2.885 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: A 667 MET cc_start: 0.8268 (tmm) cc_final: 0.8050 (tmm) REVERT: A 870 MET cc_start: 0.8452 (mmm) cc_final: 0.8181 (mmm) REVERT: B 116 LEU cc_start: 0.8397 (mt) cc_final: 0.7741 (tp) REVERT: B 176 GLU cc_start: 0.8917 (mp0) cc_final: 0.8510 (pp20) REVERT: B 282 ASN cc_start: 0.8221 (m-40) cc_final: 0.7594 (p0) REVERT: E 112 TRP cc_start: 0.7998 (m100) cc_final: 0.7580 (m100) REVERT: F 188 GLU cc_start: 0.8494 (pm20) cc_final: 0.7787 (mm-30) outliers start: 35 outliers final: 29 residues processed: 159 average time/residue: 0.3331 time to fit residues: 87.5568 Evaluate side-chains 156 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 2.997 ------------------------------------------------------------------------------- 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 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 315 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 GLU 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 874 ILE Chi-restraints excluded: chain C residue 37 ILE 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 65 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain c residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 218 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** B 841 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22731 Z= 0.163 Angle : 0.625 13.665 30806 Z= 0.306 Chirality : 0.043 0.197 3376 Planarity : 0.004 0.060 3965 Dihedral : 4.798 23.542 3013 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.31 % Allowed : 14.83 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2763 helix: 1.10 (0.18), residues: 827 sheet: -0.51 (0.19), residues: 764 loop : -1.19 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 776 HIS 0.006 0.001 HIS B 752 PHE 0.028 0.001 PHE B 174 TYR 0.015 0.001 TYR c 14 ARG 0.013 0.000 ARG F 143 ********************** 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 166 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 4.146 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: A 744 MET cc_start: 0.8616 (tmm) cc_final: 0.8394 (tmm) REVERT: A 870 MET cc_start: 0.8428 (mmm) cc_final: 0.8198 (mmm) REVERT: B 116 LEU cc_start: 0.8399 (mt) cc_final: 0.7781 (tp) REVERT: B 176 GLU cc_start: 0.8907 (mp0) cc_final: 0.8563 (pp20) REVERT: F 188 GLU cc_start: 0.8546 (pm20) cc_final: 0.7904 (mm-30) outliers start: 32 outliers final: 28 residues processed: 159 average time/residue: 0.3119 time to fit residues: 82.7657 Evaluate side-chains 154 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 334 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 749 LEU Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 341 GLU 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 C residue 37 ILE 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 65 ASP Chi-restraints excluded: chain E residue 118 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.061671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047419 restraints weight = 114882.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049048 restraints weight = 52736.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050114 restraints weight = 30962.445| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22731 Z= 0.239 Angle : 0.652 13.308 30806 Z= 0.320 Chirality : 0.044 0.215 3376 Planarity : 0.004 0.050 3965 Dihedral : 4.861 23.492 3013 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.35 % Allowed : 14.83 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2763 helix: 1.03 (0.18), residues: 833 sheet: -0.48 (0.19), residues: 768 loop : -1.13 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 112 HIS 0.005 0.001 HIS B 752 PHE 0.030 0.001 PHE B 174 TYR 0.014 0.001 TYR c 14 ARG 0.014 0.000 ARG F 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3848.70 seconds wall clock time: 70 minutes 38.01 seconds (4238.01 seconds total)