Starting phenix.real_space_refine on Sat Feb 7 17:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czj_46418/02_2026/9czj_46418_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czj_46418/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9czj_46418/02_2026/9czj_46418_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czj_46418/02_2026/9czj_46418_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9czj_46418/02_2026/9czj_46418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czj_46418/02_2026/9czj_46418.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 29 Unusual residues: {' K': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 7.02, per 1000 atoms: 0.20 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 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: 2.55 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: 6.90 Time building geometry restraints manager: 3.34 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: 17.970 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.590 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 covalent geometry : bond 0.00833 (36156) covalent geometry : angle 1.28416 (49128) SS BOND : bond 0.23869 ( 20) SS BOND : angle 15.49739 ( 40) hydrogen bonds : bond 0.17641 ( 1296) hydrogen bonds : angle 5.93383 ( 3360) Misc. bond : bond 0.65092 ( 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 : 1.101 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: 0.2173 time to fit residues: 130.0419 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 : 1.287 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 344 HIS 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 B 358 ASN 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 402 GLN 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 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 = 0.069040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051042 restraints weight = 166131.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.052793 restraints weight = 80591.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053896 restraints weight = 52912.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054580 restraints weight = 41227.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.054934 restraints weight = 35421.385| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 0.043 36179 Z= 0.145 Angle : 0.620 12.248 49168 Z= 0.310 Chirality : 0.041 0.156 5644 Planarity : 0.004 0.070 6152 Dihedral : 4.921 55.022 5004 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.13 % Favored : 95.32 % Rotamer: Outliers : 1.56 % Allowed : 9.84 % Favored : 88.60 % 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: -0.23 (0.13), residues: 4380 helix: 0.50 (0.12), residues: 2012 sheet: -0.32 (0.23), residues: 528 loop : -0.73 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 624 TYR 0.030 0.002 TYR D 401 PHE 0.038 0.002 PHE A 34 TRP 0.019 0.001 TRP H 206 HIS 0.010 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00320 (36156) covalent geometry : angle 0.61817 (49128) SS BOND : bond 0.00623 ( 20) SS BOND : angle 1.66222 ( 40) hydrogen bonds : bond 0.04078 ( 1296) hydrogen bonds : angle 4.14608 ( 3360) Misc. bond : bond 0.00344 ( 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 : 1.266 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: 0.8584 (mpp) cc_final: 0.8287 (mtt) REVERT: A 154 MET cc_start: 0.8866 (mmp) cc_final: 0.8570 (tpp) REVERT: A 892 ASP cc_start: 0.6098 (m-30) cc_final: 0.5855 (m-30) REVERT: B 154 MET cc_start: 0.8592 (mmp) cc_final: 0.8231 (tpp) REVERT: B 258 ASN cc_start: 0.7519 (m-40) cc_final: 0.7239 (m110) REVERT: B 529 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9253 (mm) REVERT: B 691 MET cc_start: 0.8505 (tpp) cc_final: 0.8242 (mmt) REVERT: C 104 MET cc_start: 0.8395 (mpp) cc_final: 0.8079 (mtm) REVERT: C 885 ASP cc_start: 0.7346 (m-30) cc_final: 0.7051 (m-30) REVERT: D 285 MET cc_start: 0.7573 (mmm) cc_final: 0.7310 (mmm) REVERT: F 204 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: H 204 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7755 (m-80) outliers start: 61 outliers final: 24 residues processed: 267 average time/residue: 0.1991 time to fit residues: 89.7923 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 : 1.367 ------------------------------------------------------------------------------- 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: 0.7980 chunk 235 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 432 optimal weight: 7.9990 chunk 131 optimal weight: 0.0070 chunk 195 optimal weight: 6.9990 chunk 362 optimal weight: 0.0020 chunk 173 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 271 optimal weight: 0.0050 overall best weight: 0.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 379 HIS A 380 ASN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN 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** E 131 HIS ** 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 = 0.3705 r_free = 0.3705 target = 0.068783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.051024 restraints weight = 165212.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052742 restraints weight = 80555.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.053839 restraints weight = 53067.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054508 restraints weight = 41314.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054871 restraints weight = 35545.606| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36179 Z= 0.110 Angle : 0.559 10.997 49168 Z= 0.278 Chirality : 0.039 0.170 5644 Planarity : 0.003 0.058 6152 Dihedral : 4.340 52.449 4988 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.59 % Favored : 94.93 % Rotamer: Outliers : 1.48 % Allowed : 10.40 % Favored : 88.11 % 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: -0.20 (0.13), residues: 4380 helix: 0.64 (0.12), residues: 2056 sheet: -0.41 (0.24), residues: 516 loop : -0.87 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 393 TYR 0.025 0.001 TYR D 401 PHE 0.040 0.001 PHE E 63 TRP 0.022 0.001 TRP G 206 HIS 0.008 0.001 HIS D 394 Details of bonding type rmsd covalent geometry : bond 0.00232 (36156) covalent geometry : angle 0.55833 (49128) SS BOND : bond 0.00212 ( 20) SS BOND : angle 0.91246 ( 40) hydrogen bonds : bond 0.03558 ( 1296) hydrogen bonds : angle 3.83491 ( 3360) Misc. bond : bond 0.00025 ( 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 263 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 1.349 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: A 34 PHE cc_start: 0.8036 (m-80) cc_final: 0.7781 (m-80) REVERT: A 104 MET cc_start: 0.8619 (mpp) cc_final: 0.8365 (mtt) REVERT: A 154 MET cc_start: 0.8870 (mmp) cc_final: 0.8526 (tpp) REVERT: A 336 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.5089 (p90) REVERT: A 892 ASP cc_start: 0.6168 (m-30) cc_final: 0.5929 (m-30) REVERT: B 104 MET cc_start: 0.8497 (mpp) cc_final: 0.8201 (mpp) REVERT: B 154 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8292 (tpp) REVERT: B 258 ASN cc_start: 0.7529 (m-40) cc_final: 0.7266 (m110) REVERT: B 422 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5727 (t) REVERT: C 104 MET cc_start: 0.8363 (mpp) cc_final: 0.8035 (mtm) REVERT: C 282 MET cc_start: 0.8919 (tpp) cc_final: 0.8707 (tpp) REVERT: C 336 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.4959 (p90) REVERT: C 885 ASP cc_start: 0.7457 (m-30) cc_final: 0.7226 (m-30) REVERT: D 21 MET cc_start: 0.7246 (mmt) cc_final: 0.6984 (mmt) REVERT: D 154 MET cc_start: 0.8515 (tpp) cc_final: 0.8049 (mmm) REVERT: D 282 MET cc_start: 0.8693 (tmm) cc_final: 0.8475 (tmm) REVERT: D 285 MET cc_start: 0.7573 (mmm) cc_final: 0.7368 (mmp) REVERT: D 409 HIS cc_start: 0.8056 (m90) cc_final: 0.7716 (m90) REVERT: E 204 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: G 204 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: H 204 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7848 (m-80) outliers start: 58 outliers final: 29 residues processed: 246 average time/residue: 0.1882 time to fit residues: 79.8324 Evaluate side-chains 227 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain B residue 154 MET 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 422 CYS 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 255 LEU Chi-restraints excluded: chain C residue 336 TYR 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 C residue 883 VAL Chi-restraints excluded: chain D residue 127 LEU 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: 6.9990 chunk 97 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 262 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 412 optimal weight: 3.9990 chunk 402 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN B 258 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 394 HIS ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 887 ASN D 893 GLN E 116 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.065581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.047183 restraints weight = 166982.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.048858 restraints weight = 81473.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049918 restraints weight = 54297.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.050566 restraints weight = 42819.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.050967 restraints weight = 37158.257| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 36179 Z= 0.225 Angle : 0.626 8.562 49168 Z= 0.313 Chirality : 0.042 0.173 5644 Planarity : 0.004 0.050 6152 Dihedral : 4.458 59.514 4981 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.21 % Favored : 94.34 % Rotamer: Outliers : 2.28 % Allowed : 10.30 % Favored : 87.42 % 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: -0.24 (0.13), residues: 4380 helix: 0.65 (0.12), residues: 2048 sheet: -0.34 (0.24), residues: 452 loop : -0.96 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 185 TYR 0.026 0.002 TYR B 401 PHE 0.038 0.002 PHE B 34 TRP 0.015 0.001 TRP G 206 HIS 0.008 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00513 (36156) covalent geometry : angle 0.62515 (49128) SS BOND : bond 0.00690 ( 20) SS BOND : angle 1.10350 ( 40) hydrogen bonds : bond 0.03670 ( 1296) hydrogen bonds : angle 3.96469 ( 3360) Misc. bond : bond 0.00074 ( 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 285 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 196 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.8086 (m-80) cc_final: 0.7884 (m-80) REVERT: A 104 MET cc_start: 0.8690 (mpp) cc_final: 0.8405 (mtt) REVERT: A 154 MET cc_start: 0.8848 (mmp) cc_final: 0.8524 (tpp) REVERT: A 204 LEU cc_start: 0.8705 (tp) cc_final: 0.8388 (tp) REVERT: A 565 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8411 (ttm) REVERT: B 799 MET cc_start: 0.8845 (tpp) cc_final: 0.8636 (tpt) REVERT: C 104 MET cc_start: 0.8474 (mpp) cc_final: 0.8092 (mpp) REVERT: C 154 MET cc_start: 0.8962 (mmm) cc_final: 0.8385 (mmm) REVERT: E 193 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4457 (tpt-90) REVERT: E 204 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: F 204 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: G 188 ASP cc_start: 0.7546 (p0) cc_final: 0.7028 (p0) REVERT: G 204 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: H 136 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: H 204 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.7823 (m-80) outliers start: 89 outliers final: 42 residues processed: 261 average time/residue: 0.2012 time to fit residues: 88.0114 Evaluate side-chains 228 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 506 MET Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET 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 906 THR Chi-restraints excluded: chain B residue 933 ILE 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 281 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 906 THR 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 314 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 393 ARG 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 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 136 GLN Chi-restraints excluded: chain H residue 162 ASN 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: 3.9990 chunk 125 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 181 optimal weight: 0.2980 chunk 349 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 184 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 363 optimal weight: 0.8980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 HIS ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.066676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.048629 restraints weight = 166859.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050331 restraints weight = 80192.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051410 restraints weight = 53012.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052077 restraints weight = 41577.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052472 restraints weight = 35937.559| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36179 Z= 0.109 Angle : 0.547 10.420 49168 Z= 0.272 Chirality : 0.039 0.151 5644 Planarity : 0.003 0.057 6152 Dihedral : 4.119 58.436 4979 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.29 % Favored : 95.30 % Rotamer: Outliers : 1.71 % Allowed : 11.25 % Favored : 87.04 % 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: -0.19 (0.13), residues: 4380 helix: 0.77 (0.12), residues: 2052 sheet: -0.76 (0.23), residues: 500 loop : -0.90 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 193 TYR 0.018 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 covalent geometry : bond 0.00233 (36156) covalent geometry : angle 0.54682 (49128) SS BOND : bond 0.00140 ( 20) SS BOND : angle 0.65976 ( 40) hydrogen bonds : bond 0.03156 ( 1296) hydrogen bonds : angle 3.76237 ( 3360) Misc. bond : bond 0.00027 ( 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 252 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8646 (mpp) cc_final: 0.8341 (mtt) REVERT: A 154 MET cc_start: 0.8823 (mmp) cc_final: 0.8569 (tpp) REVERT: A 157 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6862 (p0) REVERT: A 204 LEU cc_start: 0.8636 (tp) cc_final: 0.8308 (tp) REVERT: A 336 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5401 (p90) REVERT: A 393 ARG cc_start: 0.6125 (tpp-160) cc_final: 0.5864 (tpp-160) REVERT: A 422 CYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5760 (t) REVERT: B 422 CYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5895 (t) REVERT: C 104 MET cc_start: 0.8395 (mpp) cc_final: 0.8073 (mpp) REVERT: D 38 PHE cc_start: 0.7369 (m-10) cc_final: 0.6869 (m-80) REVERT: D 422 CYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5556 (t) REVERT: D 460 MET cc_start: 0.8542 (mmm) cc_final: 0.8220 (mmm) REVERT: E 63 PHE cc_start: 0.9155 (t80) cc_final: 0.8779 (t80) REVERT: E 204 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: F 204 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: G 54 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8887 (mm) REVERT: G 204 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: H 136 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: H 204 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.7797 (m-80) outliers start: 67 outliers final: 37 residues processed: 235 average time/residue: 0.2086 time to fit residues: 83.4834 Evaluate side-chains 223 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASN 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 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 905 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 422 CYS Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain C residue 30 MET 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 906 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 175 LEU 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 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 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 195 HIS Chi-restraints excluded: chain F residue 204 PHE Chi-restraints excluded: chain G residue 54 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 101 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 313 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 396 optimal weight: 0.7980 chunk 326 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 390 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 363 optimal weight: 2.9990 chunk 301 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.066823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048846 restraints weight = 165747.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.050546 restraints weight = 79406.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051632 restraints weight = 52315.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.052292 restraints weight = 40982.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.052575 restraints weight = 35424.831| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36179 Z= 0.101 Angle : 0.532 8.765 49168 Z= 0.262 Chirality : 0.039 0.159 5644 Planarity : 0.003 0.066 6152 Dihedral : 4.016 57.527 4979 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.47 % Favored : 95.14 % Rotamer: Outliers : 2.02 % Allowed : 11.45 % Favored : 86.53 % 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: -0.12 (0.13), residues: 4380 helix: 0.83 (0.12), residues: 2052 sheet: -0.40 (0.24), residues: 484 loop : -0.96 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 151 TYR 0.016 0.001 TYR B 401 PHE 0.037 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 covalent geometry : bond 0.00221 (36156) covalent geometry : angle 0.53160 (49128) SS BOND : bond 0.00169 ( 20) SS BOND : angle 0.82688 ( 40) hydrogen bonds : bond 0.02989 ( 1296) hydrogen bonds : angle 3.65149 ( 3360) Misc. bond : bond 0.00022 ( 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 260 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 181 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8629 (mpp) cc_final: 0.8317 (mtt) REVERT: A 154 MET cc_start: 0.8846 (mmp) cc_final: 0.8588 (tpp) REVERT: A 157 ASN cc_start: 0.7078 (OUTLIER) cc_final: 0.6841 (p0) REVERT: A 204 LEU cc_start: 0.8625 (tp) cc_final: 0.8284 (tp) REVERT: A 422 CYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5789 (t) REVERT: A 442 MET cc_start: 0.8158 (ttm) cc_final: 0.7795 (mtt) REVERT: C 104 MET cc_start: 0.8414 (mpp) cc_final: 0.8092 (mpp) REVERT: C 607 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8004 (ptp-170) REVERT: D 422 CYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5492 (t) REVERT: E 63 PHE cc_start: 0.9189 (t80) cc_final: 0.8890 (t80) REVERT: E 158 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8804 (mp0) REVERT: E 204 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: F 63 PHE cc_start: 0.9193 (t80) cc_final: 0.8624 (t80) REVERT: F 204 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: G 204 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: H 136 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: H 204 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7795 (m-80) outliers start: 79 outliers final: 43 residues processed: 245 average time/residue: 0.2002 time to fit residues: 84.2616 Evaluate side-chains 231 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 193 VAL 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 770 LEU Chi-restraints excluded: chain A residue 906 THR 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 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 394 HIS Chi-restraints excluded: chain C residue 607 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain D residue 175 LEU 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 89 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 193 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 154 optimal weight: 0.6980 chunk 55 optimal weight: 0.0670 chunk 410 optimal weight: 10.0000 chunk 433 optimal weight: 0.0670 chunk 53 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 229 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 222 GLN C 350 HIS C 379 HIS C 534 ASN ** 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** G 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.067394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049429 restraints weight = 167848.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051133 restraints weight = 80775.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052231 restraints weight = 53374.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.052894 restraints weight = 41832.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053308 restraints weight = 36171.230| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36179 Z= 0.094 Angle : 0.534 9.258 49168 Z= 0.263 Chirality : 0.039 0.162 5644 Planarity : 0.003 0.058 6152 Dihedral : 3.880 54.962 4979 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.38 % Favored : 95.25 % Rotamer: Outliers : 1.79 % Allowed : 12.01 % Favored : 86.20 % 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: 0.01 (0.13), residues: 4380 helix: 0.91 (0.12), residues: 2020 sheet: -0.78 (0.23), residues: 532 loop : -0.67 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 151 TYR 0.014 0.001 TYR B 401 PHE 0.021 0.001 PHE B 223 TRP 0.007 0.001 TRP G 206 HIS 0.005 0.001 HIS D 586 Details of bonding type rmsd covalent geometry : bond 0.00197 (36156) covalent geometry : angle 0.53409 (49128) SS BOND : bond 0.00149 ( 20) SS BOND : angle 0.74380 ( 40) hydrogen bonds : bond 0.02855 ( 1296) hydrogen bonds : angle 3.59228 ( 3360) Misc. bond : bond 0.00012 ( 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 262 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8619 (mpp) cc_final: 0.8309 (mtt) REVERT: A 154 MET cc_start: 0.8855 (mmp) cc_final: 0.8609 (tpp) REVERT: A 204 LEU cc_start: 0.8552 (tp) cc_final: 0.8203 (tp) REVERT: A 422 CYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5780 (t) REVERT: C 104 MET cc_start: 0.8364 (mpp) cc_final: 0.8091 (mpp) REVERT: C 607 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7850 (ptp-170) REVERT: D 460 MET cc_start: 0.8359 (mmm) cc_final: 0.7957 (mmm) REVERT: E 63 PHE cc_start: 0.9182 (t80) cc_final: 0.8845 (t80) REVERT: E 107 ARG cc_start: 0.7990 (mmp80) cc_final: 0.7771 (mmp80) REVERT: E 204 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: F 63 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8780 (t80) REVERT: F 158 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8908 (mm-30) REVERT: F 204 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: G 204 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: H 136 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: H 204 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.7871 (m-80) outliers start: 70 outliers final: 51 residues processed: 246 average time/residue: 0.1974 time to fit residues: 84.0989 Evaluate side-chains 241 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 193 VAL 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 770 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 175 LEU 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 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 B residue 1012 PHE Chi-restraints excluded: chain C residue 30 MET 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 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 607 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 175 LEU 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 906 THR Chi-restraints excluded: chain D residue 1017 LEU 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 63 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 193 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 159 optimal weight: 0.7980 chunk 357 optimal weight: 2.9990 chunk 426 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 360 optimal weight: 0.1980 chunk 381 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN ** 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** G 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.066993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.048997 restraints weight = 168180.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.050693 restraints weight = 81202.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051736 restraints weight = 53729.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.052423 restraints weight = 42413.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.052808 restraints weight = 36697.968| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36179 Z= 0.106 Angle : 0.535 10.504 49168 Z= 0.263 Chirality : 0.039 0.144 5644 Planarity : 0.003 0.051 6152 Dihedral : 3.857 55.006 4979 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.27 % Favored : 95.34 % Rotamer: Outliers : 1.74 % Allowed : 12.53 % Favored : 85.74 % 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: 0.04 (0.13), residues: 4380 helix: 0.92 (0.12), residues: 2012 sheet: -0.79 (0.23), residues: 532 loop : -0.63 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 151 TYR 0.017 0.001 TYR B 401 PHE 0.039 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 covalent geometry : bond 0.00236 (36156) covalent geometry : angle 0.53431 (49128) SS BOND : bond 0.00201 ( 20) SS BOND : angle 1.01517 ( 40) hydrogen bonds : bond 0.02813 ( 1296) hydrogen bonds : angle 3.54803 ( 3360) Misc. bond : bond 0.00026 ( 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 253 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 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: A 104 MET cc_start: 0.8627 (mpp) cc_final: 0.8311 (mtt) REVERT: A 204 LEU cc_start: 0.8581 (tp) cc_final: 0.8268 (tp) REVERT: A 422 CYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5983 (t) REVERT: A 691 MET cc_start: 0.8789 (mmt) cc_final: 0.8484 (mmt) REVERT: C 104 MET cc_start: 0.8388 (mpp) cc_final: 0.8117 (mpp) REVERT: D 37 LEU cc_start: 0.8334 (tp) cc_final: 0.8053 (pp) REVERT: D 422 CYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5571 (t) REVERT: E 63 PHE cc_start: 0.9210 (t80) cc_final: 0.8864 (t80) REVERT: E 158 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8849 (mp0) REVERT: E 204 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: F 63 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8569 (t80) REVERT: F 158 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8889 (mm-30) REVERT: F 204 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: G 204 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: H 40 LEU cc_start: 0.2471 (OUTLIER) cc_final: 0.2155 (pp) REVERT: H 63 PHE cc_start: 0.9144 (t80) cc_final: 0.8891 (t80) REVERT: H 136 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: H 204 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.7898 (m-80) outliers start: 68 outliers final: 50 residues processed: 236 average time/residue: 0.1939 time to fit residues: 79.6735 Evaluate side-chains 242 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 193 VAL 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 348 CYS Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 175 LEU 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 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 30 MET 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 906 THR Chi-restraints excluded: chain D residue 175 LEU 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 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 158 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 193 ARG 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 40 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 12 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 311 optimal weight: 0.5980 chunk 380 optimal weight: 8.9990 chunk 397 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN ** 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** G 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.066744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048706 restraints weight = 167382.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050390 restraints weight = 81026.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.051474 restraints weight = 53798.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.052126 restraints weight = 42326.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052517 restraints weight = 36744.862| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3578 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 : 0.537 9.536 49168 Z= 0.264 Chirality : 0.039 0.166 5644 Planarity : 0.003 0.044 6152 Dihedral : 3.851 55.328 4979 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.50 % Favored : 95.11 % Rotamer: Outliers : 1.79 % Allowed : 12.81 % Favored : 85.40 % 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: 0.06 (0.13), residues: 4380 helix: 0.91 (0.12), residues: 2016 sheet: -0.81 (0.23), residues: 508 loop : -0.59 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 151 TYR 0.014 0.001 TYR B 401 PHE 0.037 0.001 PHE D 34 TRP 0.006 0.001 TRP G 206 HIS 0.014 0.001 HIS G 195 Details of bonding type rmsd covalent geometry : bond 0.00249 (36156) covalent geometry : angle 0.53699 (49128) SS BOND : bond 0.00139 ( 20) SS BOND : angle 0.89114 ( 40) hydrogen bonds : bond 0.02811 ( 1296) hydrogen bonds : angle 3.56312 ( 3360) Misc. bond : bond 0.00031 ( 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 252 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8622 (mpp) cc_final: 0.8292 (mtt) REVERT: A 204 LEU cc_start: 0.8607 (tp) cc_final: 0.8297 (tp) REVERT: A 422 CYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5967 (t) REVERT: C 104 MET cc_start: 0.8377 (mpp) cc_final: 0.8101 (mpp) REVERT: D 37 LEU cc_start: 0.8348 (tp) cc_final: 0.8111 (pp) REVERT: D 422 CYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5588 (t) REVERT: D 460 MET cc_start: 0.8485 (mmm) cc_final: 0.8186 (mmm) REVERT: E 63 PHE cc_start: 0.9200 (t80) cc_final: 0.8836 (t80) REVERT: E 158 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8842 (mp0) REVERT: E 204 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: F 63 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8561 (t80) REVERT: F 158 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8875 (mm-30) REVERT: F 204 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: G 204 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: H 40 LEU cc_start: 0.2523 (OUTLIER) cc_final: 0.2192 (pp) REVERT: H 63 PHE cc_start: 0.9131 (t80) cc_final: 0.8817 (t80) REVERT: H 136 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: H 204 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.7925 (m-80) outliers start: 70 outliers final: 50 residues processed: 235 average time/residue: 0.1961 time to fit residues: 79.8590 Evaluate side-chains 240 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 770 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 175 LEU 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 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 30 MET 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 536 MET Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain D residue 175 LEU 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 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 158 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 193 ARG 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 40 LEU 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 411 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 352 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 157 optimal weight: 0.0770 chunk 427 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN D 465 ASN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN ** 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 = 0.3642 r_free = 0.3642 target = 0.066078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.047921 restraints weight = 167755.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049603 restraints weight = 81161.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050665 restraints weight = 53806.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051307 restraints weight = 42433.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051701 restraints weight = 36901.889| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36179 Z= 0.136 Angle : 0.550 10.052 49168 Z= 0.271 Chirality : 0.039 0.154 5644 Planarity : 0.003 0.040 6152 Dihedral : 3.925 57.966 4979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.54 % Favored : 95.02 % Rotamer: Outliers : 1.64 % Allowed : 12.99 % Favored : 85.38 % 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: 0.96 (0.12), residues: 1996 sheet: -0.86 (0.23), residues: 508 loop : -0.57 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 151 TYR 0.014 0.001 TYR B 401 PHE 0.038 0.001 PHE D 34 TRP 0.008 0.001 TRP D 263 HIS 0.018 0.001 HIS G 195 Details of bonding type rmsd covalent geometry : bond 0.00314 (36156) covalent geometry : angle 0.55015 (49128) SS BOND : bond 0.00156 ( 20) SS BOND : angle 0.87560 ( 40) hydrogen bonds : bond 0.02892 ( 1296) hydrogen bonds : angle 3.66331 ( 3360) Misc. bond : bond 0.00051 ( 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 244 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8618 (mpp) cc_final: 0.8295 (mtt) REVERT: A 204 LEU cc_start: 0.8653 (tp) cc_final: 0.8342 (tp) REVERT: A 422 CYS cc_start: 0.6313 (OUTLIER) cc_final: 0.6022 (t) REVERT: B 38 PHE cc_start: 0.7071 (m-10) cc_final: 0.6863 (m-10) REVERT: C 104 MET cc_start: 0.8418 (mpp) cc_final: 0.8109 (mpp) REVERT: C 924 MET cc_start: 0.8948 (tpp) cc_final: 0.8704 (mmm) REVERT: D 37 LEU cc_start: 0.8387 (tp) cc_final: 0.8157 (pp) REVERT: D 422 CYS cc_start: 0.6021 (OUTLIER) cc_final: 0.5665 (t) REVERT: E 63 PHE cc_start: 0.9229 (t80) cc_final: 0.8845 (t80) REVERT: E 158 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8856 (mp0) REVERT: E 204 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: F 63 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8567 (t80) REVERT: F 204 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: G 204 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: H 40 LEU cc_start: 0.2637 (OUTLIER) cc_final: 0.2304 (pp) REVERT: H 63 PHE cc_start: 0.9155 (t80) cc_final: 0.8846 (t80) REVERT: H 136 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: H 204 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.7945 (m-80) outliers start: 64 outliers final: 48 residues processed: 230 average time/residue: 0.1979 time to fit residues: 79.0812 Evaluate side-chains 232 residues out of total 3920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 177 PHE Chi-restraints excluded: chain B residue 204 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 30 MET 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 705 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain D residue 175 LEU 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 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 158 GLU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 193 ARG 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 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 40 LEU 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: 0.9980 chunk 96 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 366 optimal weight: 4.9990 chunk 413 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 117 optimal weight: 0.0770 chunk 203 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 165 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN ** 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 = 0.3653 r_free = 0.3653 target = 0.066486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.048423 restraints weight = 166305.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050106 restraints weight = 80447.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051179 restraints weight = 53379.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051839 restraints weight = 41974.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.052244 restraints weight = 36312.739| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36179 Z= 0.102 Angle : 0.549 10.421 49168 Z= 0.269 Chirality : 0.039 0.171 5644 Planarity : 0.003 0.040 6152 Dihedral : 3.877 57.098 4979 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.63 % Favored : 95.05 % Rotamer: Outliers : 1.66 % Allowed : 12.99 % Favored : 85.35 % 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: 0.07 (0.13), residues: 4380 helix: 0.94 (0.12), residues: 1996 sheet: -0.83 (0.23), residues: 508 loop : -0.57 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 107 TYR 0.014 0.001 TYR B 401 PHE 0.039 0.001 PHE D 34 TRP 0.007 0.001 TRP D 263 HIS 0.004 0.001 HIS D 586 Details of bonding type rmsd covalent geometry : bond 0.00228 (36156) covalent geometry : angle 0.54869 (49128) SS BOND : bond 0.00139 ( 20) SS BOND : angle 0.78214 ( 40) hydrogen bonds : bond 0.02817 ( 1296) hydrogen bonds : angle 3.69465 ( 3360) Misc. bond : bond 0.00027 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5865.59 seconds wall clock time: 102 minutes 50.99 seconds (6170.99 seconds total)