Starting phenix.real_space_refine on Mon Jul 6 11:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czj_46418/07_2026/9czj_46418_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czj_46418/07_2026/9czj_46418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9czj_46418/07_2026/9czj_46418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czj_46418/07_2026/9czj_46418.map" model { file = "/net/cci-nas-00/data/ceres_data/9czj_46418/07_2026/9czj_46418_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czj_46418/07_2026/9czj_46418_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 1 8.98 5 S 240 5.16 5 C 22896 2.51 5 N 5788 2.21 5 O 6400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35325 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7281 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 884} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7281 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 884} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7281 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 884} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7281 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 884} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1522 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain: "F" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1522 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain: "G" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1522 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain: "H" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1522 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.32, per 1000 atoms: 0.24 Number of scatterers: 35325 At special positions: 0 Unit cell: (146.08, 146.91, 161.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 1 19.00 S 240 16.00 O 6400 8.00 N 5788 7.00 C 22896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 422 " distance=1.50 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 422 " distance=1.50 Simple disulfide: pdb=" SG CYS C 348 " - pdb=" SG CYS C 422 " distance=1.50 Simple disulfide: pdb=" SG CYS D 348 " - pdb=" SG CYS D 422 " distance=1.50 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 114 " - pdb=" SG CYS E 143 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 102 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 114 " - pdb=" SG CYS F 143 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 149 " distance=2.03 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 106 " distance=2.03 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 143 " distance=2.04 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 143 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 36 sheets defined 44.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.561A pdb=" N LEU A 26 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 27 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 35 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 38 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 40 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 41 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 4.452A pdb=" N MET A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 135 Processing helix chain 'A' and resid 149 through 170 removed outlier: 4.161A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.711A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 3.516A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 removed outlier: 4.359A pdb=" N SER A 218 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 220 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.677A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 503 through 511 removed outlier: 4.014A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.690A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 603 through 608 removed outlier: 4.040A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 734 through 739 removed outlier: 4.609A pdb=" N MET A 739 " --> pdb=" O ASN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'A' and resid 819 through 828 Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.838A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.767A pdb=" N MET A 924 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 927 " --> pdb=" O MET A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.396A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 956 removed outlier: 3.799A pdb=" N GLU A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'B' and resid 21 through 42 removed outlier: 3.560A pdb=" N LEU B 26 " --> pdb=" O TRP B 23 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 27 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B 35 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 38 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE B 40 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.453A pdb=" N MET B 104 " --> pdb=" O TRP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 135 Processing helix chain 'B' and resid 149 through 170 removed outlier: 4.161A pdb=" N PHE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.711A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Proline residue: B 191 - end of helix removed outlier: 3.515A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 223 removed outlier: 4.358A pdb=" N SER B 218 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 220 " --> pdb=" O PHE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 298 through 318 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.678A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 486 through 499 Processing helix chain 'B' and resid 503 through 511 removed outlier: 4.014A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.690A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 603 through 608 removed outlier: 4.040A pdb=" N ALA B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 734 through 739 removed outlier: 4.610A pdb=" N MET B 739 " --> pdb=" O ASN B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 767 through 769 No H-bonds generated for 'chain 'B' and resid 767 through 769' Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'B' and resid 819 through 828 Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.838A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 917 through 929 removed outlier: 3.768A pdb=" N MET B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 927 " --> pdb=" O MET B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 4.395A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 956 removed outlier: 3.798A pdb=" N GLU B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 971 Processing helix chain 'B' and resid 996 through 1006 Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.560A pdb=" N LEU C 26 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 27 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 35 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 38 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 40 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 41 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 4.453A pdb=" N MET C 104 " --> pdb=" O TRP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 Processing helix chain 'C' and resid 149 through 170 removed outlier: 4.160A pdb=" N PHE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.712A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Proline residue: C 191 - end of helix removed outlier: 3.516A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 223 removed outlier: 4.359A pdb=" N SER C 218 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 220 " --> pdb=" O PHE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 258 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 298 through 318 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.678A pdb=" N ASP C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 433 through 450 Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 486 through 499 Processing helix chain 'C' and resid 503 through 511 removed outlier: 4.014A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.690A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 603 through 608 removed outlier: 4.040A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 624 No H-bonds generated for 'chain 'C' and resid 622 through 624' Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 734 through 739 removed outlier: 4.610A pdb=" N MET C 739 " --> pdb=" O ASN C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 765 Processing helix chain 'C' and resid 767 through 769 No H-bonds generated for 'chain 'C' and resid 767 through 769' Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'C' and resid 819 through 828 Processing helix chain 'C' and resid 873 through 875 No H-bonds generated for 'chain 'C' and resid 873 through 875' Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.838A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 917 through 929 removed outlier: 3.767A pdb=" N MET C 924 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 927 " --> pdb=" O MET C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 941 removed outlier: 4.396A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 956 removed outlier: 3.799A pdb=" N GLU C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 971 Processing helix chain 'C' and resid 996 through 1006 Processing helix chain 'D' and resid 21 through 42 removed outlier: 3.561A pdb=" N LEU D 26 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY D 35 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 38 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE D 40 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 41 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 4.453A pdb=" N MET D 104 " --> pdb=" O TRP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 135 Processing helix chain 'D' and resid 149 through 170 removed outlier: 4.160A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 181 through 199 removed outlier: 3.711A pdb=" N VAL D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Proline residue: D 191 - end of helix removed outlier: 3.515A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 223 removed outlier: 4.359A pdb=" N SER D 218 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 220 " --> pdb=" O PHE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 258 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 318 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.677A pdb=" N ASP D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 503 through 511 removed outlier: 4.014A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.691A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 603 through 608 removed outlier: 4.039A pdb=" N ALA D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 700 through 702 No H-bonds generated for 'chain 'D' and resid 700 through 702' Processing helix chain 'D' and resid 707 through 712 Processing helix chain 'D' and resid 734 through 739 removed outlier: 4.610A pdb=" N MET D 739 " --> pdb=" O ASN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 765 Processing helix chain 'D' and resid 767 through 769 No H-bonds generated for 'chain 'D' and resid 767 through 769' Processing helix chain 'D' and resid 786 through 791 Processing helix chain 'D' and resid 819 through 828 Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing helix chain 'D' and resid 885 through 890 removed outlier: 3.837A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 910 No H-bonds generated for 'chain 'D' and resid 907 through 910' Processing helix chain 'D' and resid 917 through 929 removed outlier: 3.767A pdb=" N MET D 924 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR D 927 " --> pdb=" O MET D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 941 removed outlier: 4.395A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 956 removed outlier: 3.799A pdb=" N GLU D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 971 Processing helix chain 'D' and resid 996 through 1006 Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 48 through 78 removed outlier: 3.572A pdb=" N LEU E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 197 through 226 removed outlier: 4.159A pdb=" N TRP E 206 " --> pdb=" O HIS E 202 " (cutoff:3.500A) Proline residue: E 207 - end of helix Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 48 through 78 removed outlier: 3.572A pdb=" N LEU F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 153 through 168 Processing helix chain 'F' and resid 197 through 226 removed outlier: 4.158A pdb=" N TRP F 206 " --> pdb=" O HIS F 202 " (cutoff:3.500A) Proline residue: F 207 - end of helix Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 48 through 78 removed outlier: 3.572A pdb=" N LEU G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER G 71 " --> pdb=" O PHE G 67 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 134 through 139 Processing helix chain 'G' and resid 153 through 168 Processing helix chain 'G' and resid 197 through 226 removed outlier: 4.160A pdb=" N TRP G 206 " --> pdb=" O HIS G 202 " (cutoff:3.500A) Proline residue: G 207 - end of helix Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 48 through 78 removed outlier: 3.572A pdb=" N LEU H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER H 71 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 134 through 139 Processing helix chain 'H' and resid 153 through 168 Processing helix chain 'H' and resid 197 through 226 removed outlier: 4.159A pdb=" N TRP H 206 " --> pdb=" O HIS H 202 " (cutoff:3.500A) Proline residue: H 207 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.854A pdb=" N ALA A 421 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS A 348 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 423 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG A 455 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 424 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 457 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP A 482 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N MET A 460 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 484 " --> pdb=" O MET A 460 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 535 through 540 Processing sheet with id= C, first strand: chain 'A' and resid 567 through 570 removed outlier: 3.524A pdb=" N ILE A 568 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 570 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 578 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 914 through 916 removed outlier: 7.335A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 976 through 981 Processing sheet with id= F, first strand: chain 'A' and resid 1014 through 1017 Processing sheet with id= G, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.853A pdb=" N ALA B 421 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS B 348 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 423 " --> pdb=" O CYS B 348 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG B 455 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE B 424 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 457 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP B 482 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N MET B 460 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 484 " --> pdb=" O MET B 460 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 535 through 540 Processing sheet with id= I, first strand: chain 'B' and resid 567 through 570 removed outlier: 3.525A pdb=" N ILE B 568 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 570 " --> pdb=" O ARG B 578 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 578 " --> pdb=" O TYR B 570 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 914 through 916 removed outlier: 7.335A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 976 through 981 Processing sheet with id= L, first strand: chain 'B' and resid 1014 through 1017 Processing sheet with id= M, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.854A pdb=" N ALA C 421 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS C 348 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU C 423 " --> pdb=" O CYS C 348 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG C 455 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE C 424 " --> pdb=" O ARG C 455 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE C 457 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP C 482 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N MET C 460 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 484 " --> pdb=" O MET C 460 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 535 through 540 Processing sheet with id= O, first strand: chain 'C' and resid 567 through 570 removed outlier: 3.524A pdb=" N ILE C 568 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 570 " --> pdb=" O ARG C 578 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 578 " --> pdb=" O TYR C 570 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 914 through 916 removed outlier: 7.335A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 976 through 981 Processing sheet with id= R, first strand: chain 'C' and resid 1014 through 1017 Processing sheet with id= S, first strand: chain 'D' and resid 345 through 349 removed outlier: 6.855A pdb=" N ALA D 421 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS D 348 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU D 423 " --> pdb=" O CYS D 348 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG D 455 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 424 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 457 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP D 482 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N MET D 460 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 484 " --> pdb=" O MET D 460 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 535 through 540 Processing sheet with id= U, first strand: chain 'D' and resid 567 through 570 removed outlier: 3.524A pdb=" N ILE D 568 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 570 " --> pdb=" O ARG D 578 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 578 " --> pdb=" O TYR D 570 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 914 through 916 removed outlier: 7.336A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 976 through 981 Processing sheet with id= X, first strand: chain 'D' and resid 1014 through 1017 Processing sheet with id= Y, first strand: chain 'E' and resid 79 through 82 Processing sheet with id= Z, first strand: chain 'E' and resid 95 through 99 Processing sheet with id= AA, first strand: chain 'E' and resid 188 through 190 removed outlier: 8.436A pdb=" N VAL E 189 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 129 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL E 117 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN E 116 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN E 120 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL E 86 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 79 through 82 Processing sheet with id= AC, first strand: chain 'F' and resid 95 through 99 Processing sheet with id= AD, first strand: chain 'F' and resid 188 through 190 removed outlier: 8.436A pdb=" N VAL F 189 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 129 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL F 117 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN F 116 " --> pdb=" O GLN F 90 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN F 120 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL F 86 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 79 through 82 Processing sheet with id= AF, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= AG, first strand: chain 'G' and resid 188 through 190 removed outlier: 8.436A pdb=" N VAL G 189 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU G 129 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL G 117 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN G 116 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN G 120 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL G 86 " --> pdb=" O ASN G 120 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 79 through 82 Processing sheet with id= AI, first strand: chain 'H' and resid 95 through 99 Processing sheet with id= AJ, first strand: chain 'H' and resid 188 through 190 removed outlier: 8.435A pdb=" N VAL H 189 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU H 129 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL H 117 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN H 116 " --> pdb=" O GLN H 90 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN H 120 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL H 86 " --> pdb=" O ASN H 120 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5826 1.31 - 1.44: 9756 1.44 - 1.57: 20228 1.57 - 1.70: 10 1.70 - 1.83: 336 Bond restraints: 36156 Sorted by residual: bond pdb=" N SER B 804 " pdb=" CA SER B 804 " ideal model delta sigma weight residual 1.454 1.380 0.073 1.23e-02 6.61e+03 3.53e+01 bond pdb=" N SER D 804 " pdb=" CA SER D 804 " ideal model delta sigma weight residual 1.454 1.381 0.073 1.23e-02 6.61e+03 3.49e+01 bond pdb=" N SER A 804 " pdb=" CA SER A 804 " ideal model delta sigma weight residual 1.454 1.381 0.073 1.23e-02 6.61e+03 3.48e+01 bond pdb=" N SER C 804 " pdb=" CA SER C 804 " ideal model delta sigma weight residual 1.454 1.381 0.072 1.23e-02 6.61e+03 3.44e+01 bond pdb=" C SER D 729 " pdb=" N ALA D 730 " ideal model delta sigma weight residual 1.330 1.257 0.073 1.31e-02 5.83e+03 3.14e+01 ... (remaining 36151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 44306 2.20 - 4.39: 4270 4.39 - 6.59: 480 6.59 - 8.78: 48 8.78 - 10.98: 24 Bond angle restraints: 49128 Sorted by residual: angle pdb=" C GLN H 174 " pdb=" N PRO H 175 " pdb=" CA PRO H 175 " ideal model delta sigma weight residual 119.85 112.50 7.35 1.01e+00 9.80e-01 5.29e+01 angle pdb=" C GLN G 174 " pdb=" N PRO G 175 " pdb=" CA PRO G 175 " ideal model delta sigma weight residual 119.85 112.51 7.34 1.01e+00 9.80e-01 5.29e+01 angle pdb=" C GLN E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta sigma weight residual 119.85 112.52 7.33 1.01e+00 9.80e-01 5.27e+01 angle pdb=" C GLN F 174 " pdb=" N PRO F 175 " pdb=" CA PRO F 175 " ideal model delta sigma weight residual 119.85 112.53 7.32 1.01e+00 9.80e-01 5.25e+01 angle pdb=" N HIS D 350 " pdb=" CA HIS D 350 " pdb=" C HIS D 350 " ideal model delta sigma weight residual 108.17 118.06 -9.89 1.85e+00 2.92e-01 2.86e+01 ... (remaining 49123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 20014 16.30 - 32.61: 1198 32.61 - 48.91: 296 48.91 - 65.22: 52 65.22 - 81.52: 20 Dihedral angle restraints: 21580 sinusoidal: 8636 harmonic: 12944 Sorted by residual: dihedral pdb=" CB CYS C 348 " pdb=" SG CYS C 348 " pdb=" SG CYS C 422 " pdb=" CB CYS C 422 " ideal model delta sinusoidal sigma weight residual -86.00 -140.68 54.68 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS D 348 " pdb=" SG CYS D 348 " pdb=" SG CYS D 422 " pdb=" CB CYS D 422 " ideal model delta sinusoidal sigma weight residual -86.00 -140.68 54.68 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS A 348 " pdb=" SG CYS A 348 " pdb=" SG CYS A 422 " pdb=" CB CYS A 422 " ideal model delta sinusoidal sigma weight residual -86.00 -140.66 54.66 1 1.00e+01 1.00e-02 4.05e+01 ... (remaining 21577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4742 0.100 - 0.201: 745 0.201 - 0.301: 109 0.301 - 0.401: 34 0.401 - 0.501: 14 Chirality restraints: 5644 Sorted by residual: chirality pdb=" CA GLU G 44 " pdb=" N GLU G 44 " pdb=" C GLU G 44 " pdb=" CB GLU G 44 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CA GLU E 44 " pdb=" N GLU E 44 " pdb=" C GLU E 44 " pdb=" CB GLU E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA GLU F 44 " pdb=" N GLU F 44 " pdb=" C GLU F 44 " pdb=" CB GLU F 44 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 5641 not shown) Planarity restraints: 6152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 246 " -0.098 2.00e-02 2.50e+03 5.93e-02 8.80e+01 pdb=" CG TRP D 246 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP D 246 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 246 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP D 246 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP D 246 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 246 " 0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 246 " -0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 246 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP D 246 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 246 " -0.098 2.00e-02 2.50e+03 5.93e-02 8.80e+01 pdb=" CG TRP A 246 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 246 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 246 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 246 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP A 246 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 246 " 0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 246 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 246 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP A 246 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 246 " 0.098 2.00e-02 2.50e+03 5.92e-02 8.77e+01 pdb=" CG TRP B 246 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 246 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 246 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 246 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP B 246 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 246 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 246 " 0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 246 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP B 246 " 0.068 2.00e-02 2.50e+03 ... (remaining 6149 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.86: 4 1.86 - 2.68: 713 2.68 - 3.50: 58892 3.50 - 4.32: 100987 4.32 - 5.14: 181240 Nonbonded interactions: 341836 Sorted by model distance: nonbonded pdb=" CD1 LEU D 179 " pdb=" O LYS H 46 " model vdw 1.034 3.460 nonbonded pdb=" CD1 LEU A 179 " pdb=" O LYS E 46 " model vdw 1.249 3.460 nonbonded pdb=" OD2 ASP F 187 " pdb=" NH2 ARG G 151 " model vdw 1.447 3.120 nonbonded pdb=" CD1 LEU B 179 " pdb=" O LYS F 46 " model vdw 1.592 3.460 nonbonded pdb=" OD2 ASP F 187 " pdb=" CZ ARG G 151 " model vdw 1.881 3.270 ... (remaining 341831 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 19 through 1100) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.770 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: 0.050 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.920 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.012 0.881 36179 Z= 0.831 Angle : 1.358 45.402 49168 Z= 0.858 Chirality : 0.078 0.501 5644 Planarity : 0.009 0.129 6152 Dihedral : 11.542 81.522 13128 Min Nonbonded Distance : 1.034 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.66 % Favored : 94.52 % Rotamer: Outliers : 1.43 % Allowed : 7.29 % Favored : 91.28 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4380 helix: -0.49 (0.11), residues: 1988 sheet: -0.48 (0.22), residues: 568 loop : -0.84 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 938 TYR 0.099 0.008 TYR D 928 PHE 0.085 0.006 PHE H 67 TRP 0.098 0.015 TRP A 246 HIS 0.018 0.001 HIS D 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.51 (36156) covalent geometry : angle 1.28416 / 0.83 (49128) SS BOND : bond 0.23869 / 11.96 ( 20) SS BOND : angle 15.49739 / 8.48 ( 40) hydrogen bonds : bond 0.17641 / 11.87 ( 1296) hydrogen bonds : angle 5.93383 / 4.28 ( 3360) Misc. bond : bond 0.65092 / 33.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 333 time to evaluate : 1.523 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 30 MET cc_start: 0.8418 (tpt) cc_final: 0.7969 (tpt) REVERT: A 104 MET cc_start: 0.8626 (mpp) cc_final: 0.8307 (mtt) REVERT: A 691 MET cc_start: 0.8292 (tpp) cc_final: 0.8073 (tpt) REVERT: B 30 MET cc_start: 0.8411 (tpt) cc_final: 0.8050 (tpt) REVERT: B 104 MET cc_start: 0.8580 (mpp) cc_final: 0.8220 (mpp) REVERT: B 258 ASN cc_start: 0.7568 (m-40) cc_final: 0.7268 (m110) REVERT: C 104 MET cc_start: 0.8378 (mpp) cc_final: 0.8050 (mtm) REVERT: C 282 MET cc_start: 0.9016 (tpp) cc_final: 0.8659 (tpp) REVERT: C 885 ASP cc_start: 0.7195 (m-30) cc_final: 0.6945 (m-30) REVERT: D 34 PHE cc_start: 0.8182 (m-10) cc_final: 0.7942 (m-10) REVERT: D 38 PHE cc_start: 0.7425 (m-80) cc_final: 0.7092 (m-80) REVERT: D 209 LEU cc_start: 0.8986 (mt) cc_final: 0.8629 (mp) REVERT: D 252 PHE cc_start: 0.8242 (m-80) cc_final: 0.7876 (m-10) REVERT: D 255 LEU cc_start: 0.8998 (tp) cc_final: 0.8567 (pp) REVERT: D 285 MET cc_start: 0.7412 (mmm) cc_final: 0.7085 (mmt) REVERT: D 298 THR cc_start: 0.8094 (m) cc_final: 0.6854 (m) REVERT: D 299 LEU cc_start: 0.8660 (mt) cc_final: 0.8304 (mt) REVERT: D 409 HIS cc_start: 0.8045 (m90) cc_final: 0.7645 (m90) REVERT: E 46 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.6069 (mmmt) REVERT: E 64 ILE cc_start: 0.9072 (mt) cc_final: 0.8868 (mt) REVERT: E 206 TRP cc_start: 0.8088 (m100) cc_final: 0.7790 (m100) REVERT: F 46 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7089 (mmtt) REVERT: G 64 ILE cc_start: 0.9115 (mt) cc_final: 0.8900 (mt) REVERT: G 206 TRP cc_start: 0.7969 (m100) cc_final: 0.7468 (m100) REVERT: H 46 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6919 (mmtt) outliers start: 56 outliers final: 11 residues processed: 370 average time/residue: 0.2302 time to fit residues: 138.1544 Evaluate side-chains 222 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 379 HIS A 380 ASN A 451 HIS A 471 ASN A 616 HIS ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A 979 GLN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 379 HIS B 380 ASN B 451 HIS B 471 ASN B 616 HIS ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B 907 GLN B 971 ASN B 979 GLN C 344 HIS C 358 ASN C 379 HIS C 380 ASN C 451 HIS C 471 ASN C 616 HIS ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN C 971 ASN C 979 GLN D 344 HIS D 358 ASN D 451 HIS D 471 ASN D 616 HIS ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN D 971 ASN D 979 GLN E 184 GLN E 195 HIS F 78 GLN G 78 GLN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.068997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051071 restraints weight = 165427.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052820 restraints weight = 79804.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.053927 restraints weight = 52180.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054609 restraints weight = 40486.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055031 restraints weight = 34753.641| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36179 Z= 0.146 Angle : 0.618 11.635 49168 Z= 0.309 Chirality : 0.041 0.175 5644 Planarity : 0.004 0.068 6152 Dihedral : 4.902 55.286 5004 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.16 % Favored : 95.30 % Rotamer: Outliers : 1.56 % Allowed : 9.82 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4380 helix: 0.50 (0.12), residues: 2012 sheet: -0.32 (0.23), residues: 528 loop : -0.71 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 127 TYR 0.028 0.001 TYR D 401 PHE 0.035 0.002 PHE A 34 TRP 0.019 0.001 TRP H 167 HIS 0.011 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (36156) covalent geometry : angle 0.61617 / 0.31 (49128) SS BOND : bond 0.00187 / 0.12 ( 20) SS BOND : angle 1.82315 / 0.99 ( 40) hydrogen bonds : bond 0.04173 / 2.75 ( 1296) hydrogen bonds : angle 4.13740 / 2.96 ( 3360) Misc. bond : bond 0.00145 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 1.490 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: A 104 MET cc_start: 0.8565 (mpp) cc_final: 0.8260 (mtt) REVERT: A 154 MET cc_start: 0.8839 (mmp) cc_final: 0.8547 (tpp) REVERT: A 892 ASP cc_start: 0.6097 (m-30) cc_final: 0.5863 (m-30) REVERT: B 34 PHE cc_start: 0.8158 (m-80) cc_final: 0.7819 (m-80) REVERT: B 154 MET cc_start: 0.8584 (mmp) cc_final: 0.8230 (tpp) REVERT: B 258 ASN cc_start: 0.7547 (m-40) cc_final: 0.7258 (m110) REVERT: B 529 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9257 (mm) REVERT: B 691 MET cc_start: 0.8503 (tpp) cc_final: 0.8236 (mmt) REVERT: C 104 MET cc_start: 0.8374 (mpp) cc_final: 0.8051 (mtm) REVERT: C 885 ASP cc_start: 0.7359 (m-30) cc_final: 0.7064 (m-30) REVERT: D 285 MET cc_start: 0.7574 (mmm) cc_final: 0.7292 (mmm) REVERT: E 206 TRP cc_start: 0.8368 (m100) cc_final: 0.7757 (m100) REVERT: F 204 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: H 204 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.7767 (m-80) outliers start: 61 outliers final: 24 residues processed: 265 average time/residue: 0.2089 time to fit residues: 92.8250 Evaluate side-chains 216 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 92 optimal weight: 0.8980 chunk 235 optimal weight: 0.3980 chunk 180 optimal weight: 3.9990 chunk 432 optimal weight: 6.9990 chunk 131 optimal weight: 0.0060 chunk 195 optimal weight: 0.0370 chunk 362 optimal weight: 0.0980 chunk 173 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 380 ASN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN B 344 HIS B 379 HIS B 380 ASN ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 HIS C 380 ASN ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.069252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.051575 restraints weight = 165300.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053301 restraints weight = 80465.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054398 restraints weight = 52900.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055082 restraints weight = 41135.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.055499 restraints weight = 35318.263| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36179 Z= 0.106 Angle : 0.558 10.427 49168 Z= 0.277 Chirality : 0.039 0.171 5644 Planarity : 0.003 0.056 6152 Dihedral : 4.350 51.936 4988 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.50 % Favored : 95.02 % Rotamer: Outliers : 1.33 % Allowed : 10.43 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4380 helix: 0.71 (0.12), residues: 2016 sheet: -0.62 (0.22), residues: 568 loop : -0.62 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 127 TYR 0.025 0.001 TYR D 401 PHE 0.038 0.001 PHE E 63 TRP 0.020 0.001 TRP G 206 HIS 0.009 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (36156) covalent geometry : angle 0.55739 / 0.28 (49128) SS BOND : bond 0.00173 / 0.10 ( 20) SS BOND : angle 0.93188 / 0.53 ( 40) hydrogen bonds : bond 0.03538 / 2.30 ( 1296) hydrogen bonds : angle 3.83462 / 2.75 ( 3360) Misc. bond : bond 0.00051 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 1.460 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: A 104 MET cc_start: 0.8610 (mpp) cc_final: 0.8356 (mtt) REVERT: A 154 MET cc_start: 0.8838 (mmp) cc_final: 0.8497 (tpp) REVERT: A 892 ASP cc_start: 0.6145 (m-30) cc_final: 0.5900 (m-30) REVERT: B 104 MET cc_start: 0.8471 (mpp) cc_final: 0.8154 (mpp) REVERT: B 154 MET cc_start: 0.8658 (mmp) cc_final: 0.8296 (tpp) REVERT: B 258 ASN cc_start: 0.7502 (m-40) cc_final: 0.7233 (m110) REVERT: C 104 MET cc_start: 0.8349 (mpp) cc_final: 0.8029 (mtm) REVERT: C 282 MET cc_start: 0.8895 (tpp) cc_final: 0.8694 (tpp) REVERT: C 885 ASP cc_start: 0.7367 (m-30) cc_final: 0.7130 (m-30) REVERT: D 21 MET cc_start: 0.7238 (mmt) cc_final: 0.6982 (mmt) REVERT: D 154 MET cc_start: 0.8466 (tpp) cc_final: 0.8001 (mmm) REVERT: D 285 MET cc_start: 0.7459 (mmm) cc_final: 0.7251 (mmp) REVERT: D 409 HIS cc_start: 0.8021 (m90) cc_final: 0.7661 (m90) REVERT: E 204 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: G 204 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: H 204 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7831 (m-80) outliers start: 52 outliers final: 29 residues processed: 242 average time/residue: 0.2008 time to fit residues: 83.6708 Evaluate side-chains 224 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 393 ARG Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 336 TYR Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 425 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 262 optimal weight: 0.0470 chunk 23 optimal weight: 3.9990 chunk 412 optimal weight: 8.9990 chunk 402 optimal weight: 0.0570 chunk 265 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 HIS ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN G 116 GLN H 116 GLN ** H 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.067243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049117 restraints weight = 167193.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050837 restraints weight = 81000.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.051932 restraints weight = 53563.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052593 restraints weight = 42001.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052934 restraints weight = 36357.518| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36179 Z= 0.147 Angle : 0.562 7.304 49168 Z= 0.281 Chirality : 0.040 0.190 5644 Planarity : 0.003 0.046 6152 Dihedral : 4.214 54.064 4983 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.68 % Favored : 94.86 % Rotamer: Outliers : 2.02 % Allowed : 10.51 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4380 helix: 0.73 (0.12), residues: 2052 sheet: -0.58 (0.23), residues: 516 loop : -0.87 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 127 TYR 0.024 0.001 TYR B 401 PHE 0.035 0.002 PHE F 63 TRP 0.014 0.001 TRP G 206 HIS 0.015 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (36156) covalent geometry : angle 0.56116 / 0.28 (49128) SS BOND : bond 0.00442 / 0.22 ( 20) SS BOND : angle 0.95719 / 0.55 ( 40) hydrogen bonds : bond 0.03394 / 2.19 ( 1296) hydrogen bonds : angle 3.76998 / 2.70 ( 3360) Misc. bond : bond 0.00069 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 1.279 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 104 MET cc_start: 0.8669 (mpp) cc_final: 0.8407 (mtt) REVERT: A 154 MET cc_start: 0.8866 (mmp) cc_final: 0.8571 (tpp) REVERT: A 204 LEU cc_start: 0.8518 (tp) cc_final: 0.8222 (tp) REVERT: A 336 TYR cc_start: 0.6177 (OUTLIER) cc_final: 0.5307 (p90) REVERT: A 1012 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7151 (t80) REVERT: B 104 MET cc_start: 0.8519 (mpp) cc_final: 0.8191 (mpp) REVERT: B 154 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8515 (tpp) REVERT: C 104 MET cc_start: 0.8426 (mpp) cc_final: 0.8120 (mpp) REVERT: C 336 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5089 (p90) REVERT: C 607 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (ptp-170) REVERT: D 34 PHE cc_start: 0.8347 (m-10) cc_final: 0.8108 (m-80) REVERT: D 38 PHE cc_start: 0.7318 (m-10) cc_final: 0.6913 (m-80) REVERT: D 282 MET cc_start: 0.8685 (tmm) cc_final: 0.8416 (tpp) REVERT: E 204 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: F 204 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: G 204 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: H 204 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.7819 (m-80) outliers start: 79 outliers final: 40 residues processed: 261 average time/residue: 0.2128 time to fit residues: 93.2641 Evaluate side-chains 230 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 1012 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 422 CYS Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 306 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 181 optimal weight: 0.2980 chunk 349 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 184 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 324 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS A 379 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 HIS ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.049824 restraints weight = 166304.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051556 restraints weight = 79608.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.052621 restraints weight = 52240.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053320 restraints weight = 40863.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053745 restraints weight = 35160.589| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36179 Z= 0.102 Angle : 0.538 10.312 49168 Z= 0.266 Chirality : 0.039 0.165 5644 Planarity : 0.003 0.057 6152 Dihedral : 4.012 51.831 4981 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.36 % Favored : 95.23 % Rotamer: Outliers : 1.69 % Allowed : 11.53 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4380 helix: 0.80 (0.12), residues: 2052 sheet: -0.59 (0.23), residues: 516 loop : -0.91 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 393 TYR 0.017 0.001 TYR B 401 PHE 0.039 0.001 PHE B 34 TRP 0.012 0.001 TRP G 206 HIS 0.006 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (36156) covalent geometry : angle 0.53792 / 0.27 (49128) SS BOND : bond 0.00150 / 0.09 ( 20) SS BOND : angle 0.63705 / 0.37 ( 40) hydrogen bonds : bond 0.03063 / 1.98 ( 1296) hydrogen bonds : angle 3.67332 / 2.63 ( 3360) Misc. bond : bond 0.00022 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8628 (mpp) cc_final: 0.8341 (mtt) REVERT: A 204 LEU cc_start: 0.8501 (tp) cc_final: 0.8185 (tp) REVERT: A 393 ARG cc_start: 0.6061 (tpp-160) cc_final: 0.5778 (tpp-160) REVERT: A 422 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5805 (t) REVERT: B 104 MET cc_start: 0.8478 (mpp) cc_final: 0.8203 (mpp) REVERT: B 258 ASN cc_start: 0.7245 (m110) cc_final: 0.6712 (p0) REVERT: B 607 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8033 (ttm170) REVERT: C 104 MET cc_start: 0.8306 (mpp) cc_final: 0.8058 (mpp) REVERT: C 422 CYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5975 (t) REVERT: C 607 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7997 (ptp-170) REVERT: D 38 PHE cc_start: 0.7254 (m-10) cc_final: 0.6796 (m-80) REVERT: D 460 MET cc_start: 0.8523 (mmm) cc_final: 0.8175 (mmm) REVERT: E 158 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: E 204 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: F 204 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: G 204 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: H 204 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.7765 (m-80) outliers start: 66 outliers final: 33 residues processed: 243 average time/residue: 0.1967 time to fit residues: 81.1351 Evaluate side-chains 222 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 422 CYS Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 313 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 396 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 390 optimal weight: 6.9990 chunk 184 optimal weight: 0.0040 chunk 363 optimal weight: 0.5980 chunk 301 optimal weight: 0.0010 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS D 379 HIS ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.067947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050138 restraints weight = 166730.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.051868 restraints weight = 79802.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.052966 restraints weight = 52426.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.053628 restraints weight = 40970.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.053945 restraints weight = 35300.532| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36179 Z= 0.096 Angle : 0.533 12.332 49168 Z= 0.263 Chirality : 0.039 0.148 5644 Planarity : 0.003 0.053 6152 Dihedral : 3.919 50.416 4981 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.47 % Favored : 95.16 % Rotamer: Outliers : 1.79 % Allowed : 11.73 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4380 helix: 0.83 (0.12), residues: 2056 sheet: -0.24 (0.24), residues: 484 loop : -0.91 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 151 TYR 0.019 0.001 TYR B 401 PHE 0.041 0.001 PHE C 34 TRP 0.008 0.001 TRP G 206 HIS 0.005 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (36156) covalent geometry : angle 0.53298 / 0.26 (49128) SS BOND : bond 0.00160 / 0.10 ( 20) SS BOND : angle 0.81168 / 0.47 ( 40) hydrogen bonds : bond 0.02919 / 1.87 ( 1296) hydrogen bonds : angle 3.60477 / 2.59 ( 3360) Misc. bond : bond 0.00026 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8629 (mpp) cc_final: 0.8333 (mtt) REVERT: A 204 LEU cc_start: 0.8476 (tp) cc_final: 0.8139 (tp) REVERT: A 422 CYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5826 (t) REVERT: B 104 MET cc_start: 0.8566 (mpp) cc_final: 0.8263 (mpp) REVERT: B 258 ASN cc_start: 0.7240 (m110) cc_final: 0.7021 (m-40) REVERT: C 104 MET cc_start: 0.8361 (mpp) cc_final: 0.8111 (mpp) REVERT: C 607 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7950 (ptp-170) REVERT: D 38 PHE cc_start: 0.7135 (m-10) cc_final: 0.6742 (m-80) REVERT: D 154 MET cc_start: 0.8521 (tpp) cc_final: 0.8306 (tpp) REVERT: D 422 CYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5692 (t) REVERT: D 924 MET cc_start: 0.8826 (tpp) cc_final: 0.8536 (tpp) REVERT: E 204 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: F 63 PHE cc_start: 0.9158 (t80) cc_final: 0.8789 (t80) REVERT: F 204 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: G 204 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: H 204 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7779 (m-80) outliers start: 70 outliers final: 45 residues processed: 242 average time/residue: 0.1975 time to fit residues: 83.0844 Evaluate side-chains 236 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 154 optimal weight: 0.1980 chunk 55 optimal weight: 10.0000 chunk 410 optimal weight: 5.9990 chunk 433 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 887 ASN E 116 GLN E 195 HIS ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.066301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048207 restraints weight = 167173.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050666 restraints weight = 81150.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051223 restraints weight = 45142.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.051497 restraints weight = 39229.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.051558 restraints weight = 37440.582| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36179 Z= 0.166 Angle : 0.559 9.786 49168 Z= 0.278 Chirality : 0.040 0.159 5644 Planarity : 0.003 0.043 6152 Dihedral : 4.043 54.511 4981 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.68 % Favored : 94.91 % Rotamer: Outliers : 1.89 % Allowed : 11.86 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4380 helix: 0.83 (0.12), residues: 2060 sheet: -0.34 (0.24), residues: 476 loop : -0.92 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 107 TYR 0.016 0.001 TYR B 401 PHE 0.041 0.002 PHE C 34 TRP 0.008 0.001 TRP C 178 HIS 0.022 0.001 HIS G 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (36156) covalent geometry : angle 0.55840 / 0.28 (49128) SS BOND : bond 0.00501 / 0.25 ( 20) SS BOND : angle 0.99800 / 0.56 ( 40) hydrogen bonds : bond 0.03099 / 2.00 ( 1296) hydrogen bonds : angle 3.69669 / 2.65 ( 3360) Misc. bond : bond 0.00064 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8681 (mpp) cc_final: 0.8378 (mtt) REVERT: A 204 LEU cc_start: 0.8641 (tp) cc_final: 0.8278 (tp) REVERT: A 422 CYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5982 (t) REVERT: B 104 MET cc_start: 0.8649 (mpp) cc_final: 0.8311 (mpp) REVERT: B 258 ASN cc_start: 0.7278 (m110) cc_final: 0.6843 (p0) REVERT: B 924 MET cc_start: 0.8889 (tpp) cc_final: 0.8628 (tpp) REVERT: C 104 MET cc_start: 0.8452 (mpp) cc_final: 0.8145 (mpp) REVERT: D 422 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5840 (t) REVERT: D 799 MET cc_start: 0.9003 (tpp) cc_final: 0.8543 (tpt) REVERT: E 158 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: E 204 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: F 63 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8622 (t80) REVERT: F 204 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: G 67 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: G 204 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: H 204 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7851 (m-80) outliers start: 74 outliers final: 45 residues processed: 233 average time/residue: 0.1773 time to fit residues: 71.9515 Evaluate side-chains 229 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 159 optimal weight: 0.3980 chunk 357 optimal weight: 2.9990 chunk 426 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 360 optimal weight: 2.9990 chunk 381 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.066763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048746 restraints weight = 166785.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.050432 restraints weight = 80142.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051509 restraints weight = 52892.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052165 restraints weight = 41505.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.052506 restraints weight = 35945.800| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36179 Z= 0.108 Angle : 0.545 10.589 49168 Z= 0.268 Chirality : 0.039 0.157 5644 Planarity : 0.003 0.039 6152 Dihedral : 3.970 53.917 4981 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.57 % Favored : 95.02 % Rotamer: Outliers : 1.71 % Allowed : 12.12 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4380 helix: 1.04 (0.12), residues: 1976 sheet: -0.73 (0.23), residues: 524 loop : -0.60 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 151 TYR 0.015 0.001 TYR B 401 PHE 0.043 0.001 PHE C 34 TRP 0.006 0.001 TRP G 206 HIS 0.011 0.001 HIS G 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (36156) covalent geometry : angle 0.54464 / 0.27 (49128) SS BOND : bond 0.00143 / 0.09 ( 20) SS BOND : angle 0.80208 / 0.45 ( 40) hydrogen bonds : bond 0.02917 / 1.88 ( 1296) hydrogen bonds : angle 3.64857 / 2.63 ( 3360) Misc. bond : bond 0.00031 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8632 (mpp) cc_final: 0.8317 (mtt) REVERT: A 204 LEU cc_start: 0.8603 (tp) cc_final: 0.8269 (tp) REVERT: A 422 CYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5928 (t) REVERT: B 104 MET cc_start: 0.8561 (mpp) cc_final: 0.8242 (mpp) REVERT: B 258 ASN cc_start: 0.7273 (m110) cc_final: 0.7023 (m-40) REVERT: C 104 MET cc_start: 0.8411 (mpp) cc_final: 0.8123 (mpp) REVERT: D 422 CYS cc_start: 0.5946 (OUTLIER) cc_final: 0.5635 (t) REVERT: E 63 PHE cc_start: 0.9179 (t80) cc_final: 0.8927 (t80) REVERT: E 158 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8881 (mp0) REVERT: E 204 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: F 63 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8565 (t80) REVERT: F 204 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: G 204 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: H 204 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7879 (m-80) outliers start: 67 outliers final: 48 residues processed: 227 average time/residue: 0.1865 time to fit residues: 73.9366 Evaluate side-chains 233 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 12 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 342 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 333 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 311 optimal weight: 0.6980 chunk 380 optimal weight: 0.6980 chunk 397 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.066780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048804 restraints weight = 165925.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.050481 restraints weight = 79714.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051564 restraints weight = 52632.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052224 restraints weight = 41183.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.052620 restraints weight = 35605.123| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36179 Z= 0.109 Angle : 0.547 10.248 49168 Z= 0.269 Chirality : 0.039 0.140 5644 Planarity : 0.003 0.040 6152 Dihedral : 3.880 53.903 4979 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.68 % Favored : 94.91 % Rotamer: Outliers : 1.41 % Allowed : 12.63 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 4380 helix: 1.00 (0.12), residues: 1988 sheet: -0.76 (0.23), residues: 500 loop : -0.53 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 151 TYR 0.014 0.001 TYR D 336 PHE 0.023 0.001 PHE C 34 TRP 0.008 0.001 TRP G 206 HIS 0.004 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (36156) covalent geometry : angle 0.54718 / 0.27 (49128) SS BOND : bond 0.00138 / 0.08 ( 20) SS BOND : angle 0.75823 / 0.43 ( 40) hydrogen bonds : bond 0.02875 / 1.85 ( 1296) hydrogen bonds : angle 3.66827 / 2.65 ( 3360) Misc. bond : bond 0.00033 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8604 (mpp) cc_final: 0.8288 (mtt) REVERT: A 204 LEU cc_start: 0.8616 (tp) cc_final: 0.8308 (tp) REVERT: A 422 CYS cc_start: 0.6285 (OUTLIER) cc_final: 0.5960 (t) REVERT: B 104 MET cc_start: 0.8533 (mpp) cc_final: 0.8241 (mpp) REVERT: B 258 ASN cc_start: 0.7311 (m110) cc_final: 0.7048 (m-40) REVERT: B 799 MET cc_start: 0.9033 (tpt) cc_final: 0.8747 (tpp) REVERT: C 104 MET cc_start: 0.8392 (mpp) cc_final: 0.8114 (mpp) REVERT: C 924 MET cc_start: 0.8882 (tpp) cc_final: 0.8601 (mmm) REVERT: D 37 LEU cc_start: 0.8380 (tp) cc_final: 0.8088 (pp) REVERT: E 63 PHE cc_start: 0.9192 (t80) cc_final: 0.8948 (t80) REVERT: E 158 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8866 (mp0) REVERT: E 204 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: F 63 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8557 (t80) REVERT: F 204 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: G 134 GLU cc_start: 0.8927 (tp30) cc_final: 0.8719 (tp30) REVERT: G 204 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: H 204 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.7912 (m-80) outliers start: 55 outliers final: 40 residues processed: 224 average time/residue: 0.1873 time to fit residues: 73.6493 Evaluate side-chains 224 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 411 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 347 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 427 optimal weight: 6.9990 chunk 395 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.065768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047508 restraints weight = 167714.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049179 restraints weight = 81165.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050235 restraints weight = 53932.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.050869 restraints weight = 42562.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.051263 restraints weight = 37110.404| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36179 Z= 0.149 Angle : 0.570 9.983 49168 Z= 0.281 Chirality : 0.039 0.168 5644 Planarity : 0.003 0.047 6152 Dihedral : 3.997 57.872 4979 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.68 % Favored : 94.89 % Rotamer: Outliers : 1.30 % Allowed : 12.68 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4380 helix: 1.03 (0.12), residues: 1972 sheet: -0.86 (0.23), residues: 500 loop : -0.55 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 393 TYR 0.015 0.001 TYR B 401 PHE 0.025 0.001 PHE G 63 TRP 0.010 0.001 TRP D 263 HIS 0.016 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (36156) covalent geometry : angle 0.56940 / 0.28 (49128) SS BOND : bond 0.00214 / 0.11 ( 20) SS BOND : angle 0.81787 / 0.47 ( 40) hydrogen bonds : bond 0.03008 / 1.95 ( 1296) hydrogen bonds : angle 3.74444 / 2.69 ( 3360) Misc. bond : bond 0.00066 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8632 (mpp) cc_final: 0.8299 (mtt) REVERT: A 204 LEU cc_start: 0.8715 (tp) cc_final: 0.8397 (tp) REVERT: A 422 CYS cc_start: 0.6324 (OUTLIER) cc_final: 0.6029 (t) REVERT: B 38 PHE cc_start: 0.7074 (m-10) cc_final: 0.6868 (m-10) REVERT: B 104 MET cc_start: 0.8590 (mpp) cc_final: 0.8288 (mpp) REVERT: B 258 ASN cc_start: 0.7227 (m110) cc_final: 0.6942 (m-40) REVERT: B 799 MET cc_start: 0.9078 (tpt) cc_final: 0.8770 (tpp) REVERT: C 104 MET cc_start: 0.8439 (mpp) cc_final: 0.8123 (mpp) REVERT: C 799 MET cc_start: 0.9148 (tpp) cc_final: 0.8917 (tpp) REVERT: C 924 MET cc_start: 0.8884 (tpp) cc_final: 0.8611 (mmm) REVERT: D 422 CYS cc_start: 0.6267 (OUTLIER) cc_final: 0.6037 (t) REVERT: E 63 PHE cc_start: 0.9206 (t80) cc_final: 0.8961 (t80) REVERT: E 158 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: E 204 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: F 63 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8596 (t80) REVERT: F 204 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: G 204 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: H 63 PHE cc_start: 0.9137 (t80) cc_final: 0.8800 (t80) REVERT: H 136 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: H 204 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.7945 (m-80) outliers start: 51 outliers final: 40 residues processed: 219 average time/residue: 0.1884 time to fit residues: 72.3963 Evaluate side-chains 225 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 906 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 195 HIS Chi-restraints excluded: chain G residue 204 PHE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 136 GLN Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 204 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 413 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 117 optimal weight: 0.0770 chunk 203 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** 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 = 0.3648 r_free = 0.3648 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.048367 restraints weight = 165783.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.050815 restraints weight = 81127.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051364 restraints weight = 44792.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051604 restraints weight = 39769.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051674 restraints weight = 37572.528| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36179 Z= 0.103 Angle : 0.549 10.599 49168 Z= 0.268 Chirality : 0.039 0.176 5644 Planarity : 0.003 0.042 6152 Dihedral : 3.915 56.796 4979 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.98 % Favored : 94.68 % Rotamer: Outliers : 1.28 % Allowed : 12.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4380 helix: 1.03 (0.12), residues: 1968 sheet: -0.84 (0.23), residues: 500 loop : -0.50 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 107 TYR 0.014 0.001 TYR D 336 PHE 0.020 0.001 PHE B 223 TRP 0.008 0.001 TRP D 263 HIS 0.010 0.001 HIS G 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (36156) covalent geometry : angle 0.54853 / 0.27 (49128) SS BOND : bond 0.00144 / 0.09 ( 20) SS BOND : angle 0.68939 / 0.39 ( 40) hydrogen bonds : bond 0.02858 / 1.84 ( 1296) hydrogen bonds : angle 3.69977 / 2.65 ( 3360) Misc. bond : bond 0.00030 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5595.36 seconds wall clock time: 98 minutes 0.86 seconds (5880.86 seconds total)