Starting phenix.real_space_refine on Thu Nov 20 22:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9op8_70682/11_2025/9op8_70682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9op8_70682/11_2025/9op8_70682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9op8_70682/11_2025/9op8_70682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9op8_70682/11_2025/9op8_70682.map" model { file = "/net/cci-nas-00/data/ceres_data/9op8_70682/11_2025/9op8_70682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9op8_70682/11_2025/9op8_70682.cif" } resolution = 3.8 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= 0.004 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 25236 2.51 5 N 7188 2.21 5 O 7104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39636 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "b" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "c" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "d" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "e" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "f" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "g" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "h" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "i" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "j" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "k" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "l" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Time building chain proxies: 9.46, per 1000 atoms: 0.24 Number of scatterers: 39636 At special positions: 0 Unit cell: (159.5, 159.5, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 7104 8.00 N 7188 7.00 C 25236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.9 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 58 sheets defined 64.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'a' and resid 33 through 44 removed outlier: 3.795A pdb=" N MET a 37 " --> pdb=" O THR a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 54 Processing helix chain 'a' and resid 55 through 60 removed outlier: 3.532A pdb=" N VAL a 59 " --> pdb=" O VAL a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 79 Processing helix chain 'a' and resid 82 through 98 Processing helix chain 'a' and resid 100 through 109 Processing helix chain 'a' and resid 112 through 147 Processing helix chain 'a' and resid 156 through 167 Processing helix chain 'a' and resid 179 through 191 removed outlier: 3.630A pdb=" N LYS a 190 " --> pdb=" O ARG a 186 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN a 191 " --> pdb=" O ALA a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 Processing helix chain 'a' and resid 198 through 221 Proline residue: a 210 - end of helix Processing helix chain 'a' and resid 271 through 297 Proline residue: a 278 - end of helix removed outlier: 3.689A pdb=" N ASN a 297 " --> pdb=" O CYS a 293 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 541 Processing helix chain 'a' and resid 558 through 573 Proline residue: a 568 - end of helix Processing helix chain 'a' and resid 585 through 590 removed outlier: 4.251A pdb=" N ILE a 589 " --> pdb=" O GLY a 585 " (cutoff:3.500A) Processing helix chain 'a' and resid 591 through 603 Processing helix chain 'a' and resid 604 through 623 removed outlier: 3.533A pdb=" N TYR a 608 " --> pdb=" O ARG a 604 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 44 removed outlier: 3.772A pdb=" N MET b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 54 Processing helix chain 'b' and resid 55 through 60 removed outlier: 3.644A pdb=" N VAL b 59 " --> pdb=" O VAL b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 80 removed outlier: 3.924A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 98 Processing helix chain 'b' and resid 100 through 109 Processing helix chain 'b' and resid 112 through 147 removed outlier: 3.541A pdb=" N ILE b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 156 through 167 Processing helix chain 'b' and resid 179 through 191 Processing helix chain 'b' and resid 193 through 197 Processing helix chain 'b' and resid 198 through 221 Proline residue: b 210 - end of helix Processing helix chain 'b' and resid 271 through 297 Proline residue: b 278 - end of helix removed outlier: 3.656A pdb=" N ASN b 297 " --> pdb=" O CYS b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 501 through 503 No H-bonds generated for 'chain 'b' and resid 501 through 503' Processing helix chain 'b' and resid 521 through 540 Processing helix chain 'b' and resid 558 through 573 Proline residue: b 568 - end of helix Processing helix chain 'b' and resid 585 through 590 removed outlier: 4.419A pdb=" N ILE b 589 " --> pdb=" O GLY b 585 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU b 590 " --> pdb=" O SER b 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 585 through 590' Processing helix chain 'b' and resid 591 through 602 Processing helix chain 'b' and resid 604 through 623 removed outlier: 3.753A pdb=" N TYR b 608 " --> pdb=" O ARG b 604 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 44 removed outlier: 3.760A pdb=" N MET c 37 " --> pdb=" O THR c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 54 Processing helix chain 'c' and resid 55 through 60 removed outlier: 3.534A pdb=" N VAL c 59 " --> pdb=" O VAL c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 80 removed outlier: 3.537A pdb=" N THR c 66 " --> pdb=" O SER c 62 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 98 Processing helix chain 'c' and resid 100 through 109 Processing helix chain 'c' and resid 112 through 147 removed outlier: 3.585A pdb=" N ILE c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 156 through 167 Processing helix chain 'c' and resid 179 through 192 removed outlier: 3.609A pdb=" N LYS c 190 " --> pdb=" O ARG c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 193 through 198 Processing helix chain 'c' and resid 198 through 221 Proline residue: c 210 - end of helix Processing helix chain 'c' and resid 271 through 297 Proline residue: c 278 - end of helix removed outlier: 3.694A pdb=" N ASN c 297 " --> pdb=" O CYS c 293 " (cutoff:3.500A) Processing helix chain 'c' and resid 501 through 503 No H-bonds generated for 'chain 'c' and resid 501 through 503' Processing helix chain 'c' and resid 521 through 541 Processing helix chain 'c' and resid 558 through 573 Proline residue: c 568 - end of helix Processing helix chain 'c' and resid 585 through 590 removed outlier: 4.255A pdb=" N ILE c 589 " --> pdb=" O GLY c 585 " (cutoff:3.500A) Processing helix chain 'c' and resid 591 through 602 Processing helix chain 'c' and resid 604 through 622 removed outlier: 4.089A pdb=" N TYR c 608 " --> pdb=" O ARG c 604 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 45 removed outlier: 3.754A pdb=" N MET d 37 " --> pdb=" O THR d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 54 Processing helix chain 'd' and resid 55 through 60 removed outlier: 3.634A pdb=" N VAL d 59 " --> pdb=" O VAL d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 80 removed outlier: 3.739A pdb=" N ALA d 80 " --> pdb=" O ALA d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 98 Processing helix chain 'd' and resid 100 through 109 Processing helix chain 'd' and resid 112 through 147 Processing helix chain 'd' and resid 148 through 150 No H-bonds generated for 'chain 'd' and resid 148 through 150' Processing helix chain 'd' and resid 156 through 167 Processing helix chain 'd' and resid 179 through 191 removed outlier: 3.643A pdb=" N LYS d 190 " --> pdb=" O ARG d 186 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN d 191 " --> pdb=" O ALA d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 198 removed outlier: 4.277A pdb=" N ARG d 196 " --> pdb=" O HIS d 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 221 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 271 through 297 Proline residue: d 278 - end of helix removed outlier: 3.704A pdb=" N ASN d 297 " --> pdb=" O CYS d 293 " (cutoff:3.500A) Processing helix chain 'd' and resid 521 through 540 Processing helix chain 'd' and resid 558 through 573 Proline residue: d 568 - end of helix Processing helix chain 'd' and resid 584 through 590 removed outlier: 3.885A pdb=" N VAL d 588 " --> pdb=" O THR d 584 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE d 589 " --> pdb=" O GLY d 585 " (cutoff:3.500A) Processing helix chain 'd' and resid 592 through 603 Processing helix chain 'd' and resid 604 through 623 removed outlier: 4.048A pdb=" N TYR d 608 " --> pdb=" O ARG d 604 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA d 623 " --> pdb=" O ASP d 619 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 44 removed outlier: 3.887A pdb=" N MET e 37 " --> pdb=" O THR e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 54 Processing helix chain 'e' and resid 55 through 60 Processing helix chain 'e' and resid 62 through 80 removed outlier: 3.562A pdb=" N THR e 66 " --> pdb=" O SER e 62 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA e 80 " --> pdb=" O ALA e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 98 Processing helix chain 'e' and resid 100 through 109 Processing helix chain 'e' and resid 112 through 147 Processing helix chain 'e' and resid 148 through 150 No H-bonds generated for 'chain 'e' and resid 148 through 150' Processing helix chain 'e' and resid 156 through 167 Processing helix chain 'e' and resid 179 through 190 removed outlier: 3.555A pdb=" N GLN e 183 " --> pdb=" O GLY e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 193 through 198 Processing helix chain 'e' and resid 198 through 221 Proline residue: e 210 - end of helix Processing helix chain 'e' and resid 271 through 297 Proline residue: e 278 - end of helix removed outlier: 3.716A pdb=" N ASN e 297 " --> pdb=" O CYS e 293 " (cutoff:3.500A) Processing helix chain 'e' and resid 499 through 503 removed outlier: 4.163A pdb=" N SER e 502 " --> pdb=" O VAL e 499 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET e 503 " --> pdb=" O SER e 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 499 through 503' Processing helix chain 'e' and resid 521 through 541 removed outlier: 3.600A pdb=" N PHE e 540 " --> pdb=" O LEU e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 558 through 573 Proline residue: e 568 - end of helix Processing helix chain 'e' and resid 585 through 590 removed outlier: 4.393A pdb=" N ILE e 589 " --> pdb=" O GLY e 585 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU e 590 " --> pdb=" O SER e 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 585 through 590' Processing helix chain 'e' and resid 591 through 603 Processing helix chain 'e' and resid 604 through 623 removed outlier: 4.191A pdb=" N TYR e 608 " --> pdb=" O ARG e 604 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU e 609 " --> pdb=" O LEU e 605 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 45 removed outlier: 3.792A pdb=" N MET f 37 " --> pdb=" O THR f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 54 Processing helix chain 'f' and resid 55 through 60 Processing helix chain 'f' and resid 62 through 79 Processing helix chain 'f' and resid 82 through 98 Processing helix chain 'f' and resid 100 through 109 Processing helix chain 'f' and resid 112 through 147 Processing helix chain 'f' and resid 148 through 150 No H-bonds generated for 'chain 'f' and resid 148 through 150' Processing helix chain 'f' and resid 156 through 167 Processing helix chain 'f' and resid 179 through 190 Processing helix chain 'f' and resid 192 through 198 removed outlier: 4.230A pdb=" N ARG f 196 " --> pdb=" O HIS f 192 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU f 198 " --> pdb=" O LEU f 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 198 through 221 Proline residue: f 210 - end of helix Processing helix chain 'f' and resid 271 through 297 Proline residue: f 278 - end of helix removed outlier: 3.514A pdb=" N ARG f 296 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN f 297 " --> pdb=" O CYS f 293 " (cutoff:3.500A) Processing helix chain 'f' and resid 501 through 503 No H-bonds generated for 'chain 'f' and resid 501 through 503' Processing helix chain 'f' and resid 521 through 541 removed outlier: 3.730A pdb=" N PHE f 540 " --> pdb=" O LEU f 536 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 572 Proline residue: f 568 - end of helix Processing helix chain 'f' and resid 584 through 588 removed outlier: 3.551A pdb=" N VAL f 588 " --> pdb=" O GLY f 585 " (cutoff:3.500A) Processing helix chain 'f' and resid 591 through 603 Processing helix chain 'f' and resid 604 through 623 removed outlier: 3.863A pdb=" N TYR f 608 " --> pdb=" O ARG f 604 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 45 removed outlier: 3.779A pdb=" N MET g 37 " --> pdb=" O THR g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 54 Processing helix chain 'g' and resid 55 through 60 Processing helix chain 'g' and resid 62 through 80 removed outlier: 3.932A pdb=" N ALA g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 98 Processing helix chain 'g' and resid 100 through 109 Processing helix chain 'g' and resid 112 through 147 Processing helix chain 'g' and resid 156 through 167 Processing helix chain 'g' and resid 179 through 192 Processing helix chain 'g' and resid 193 through 198 removed outlier: 3.674A pdb=" N GLN g 197 " --> pdb=" O PRO g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 198 through 221 Proline residue: g 210 - end of helix Processing helix chain 'g' and resid 271 through 297 Proline residue: g 278 - end of helix removed outlier: 3.684A pdb=" N ASN g 297 " --> pdb=" O CYS g 293 " (cutoff:3.500A) Processing helix chain 'g' and resid 521 through 541 Processing helix chain 'g' and resid 558 through 566 Processing helix chain 'g' and resid 566 through 573 Processing helix chain 'g' and resid 584 through 590 Processing helix chain 'g' and resid 591 through 602 Processing helix chain 'g' and resid 603 through 623 removed outlier: 4.376A pdb=" N THR g 607 " --> pdb=" O THR g 603 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR g 608 " --> pdb=" O ARG g 604 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 45 removed outlier: 3.522A pdb=" N MET h 37 " --> pdb=" O THR h 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG h 40 " --> pdb=" O THR h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 50 through 54 Processing helix chain 'h' and resid 55 through 60 removed outlier: 3.556A pdb=" N VAL h 59 " --> pdb=" O VAL h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 80 removed outlier: 3.800A pdb=" N ALA h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 98 Processing helix chain 'h' and resid 100 through 109 Processing helix chain 'h' and resid 112 through 147 Processing helix chain 'h' and resid 148 through 150 No H-bonds generated for 'chain 'h' and resid 148 through 150' Processing helix chain 'h' and resid 156 through 167 removed outlier: 3.681A pdb=" N TRP h 163 " --> pdb=" O LYS h 159 " (cutoff:3.500A) Processing helix chain 'h' and resid 179 through 190 removed outlier: 3.639A pdb=" N LYS h 190 " --> pdb=" O ARG h 186 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 198 removed outlier: 4.323A pdb=" N ARG h 196 " --> pdb=" O HIS h 192 " (cutoff:3.500A) Processing helix chain 'h' and resid 198 through 221 Proline residue: h 210 - end of helix Processing helix chain 'h' and resid 271 through 297 Proline residue: h 278 - end of helix removed outlier: 3.711A pdb=" N ASN h 297 " --> pdb=" O CYS h 293 " (cutoff:3.500A) Processing helix chain 'h' and resid 499 through 503 removed outlier: 4.221A pdb=" N SER h 502 " --> pdb=" O VAL h 499 " (cutoff:3.500A) Processing helix chain 'h' and resid 521 through 541 removed outlier: 3.799A pdb=" N PHE h 540 " --> pdb=" O LEU h 536 " (cutoff:3.500A) Processing helix chain 'h' and resid 558 through 572 Proline residue: h 568 - end of helix Processing helix chain 'h' and resid 585 through 590 removed outlier: 4.176A pdb=" N ILE h 589 " --> pdb=" O GLY h 585 " (cutoff:3.500A) Processing helix chain 'h' and resid 591 through 603 Processing helix chain 'h' and resid 603 through 623 removed outlier: 3.978A pdb=" N THR h 607 " --> pdb=" O THR h 603 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 44 removed outlier: 3.735A pdb=" N MET i 37 " --> pdb=" O THR i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 54 Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 80 removed outlier: 3.935A pdb=" N ALA i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 98 Processing helix chain 'i' and resid 100 through 109 Processing helix chain 'i' and resid 112 through 147 Processing helix chain 'i' and resid 156 through 167 Processing helix chain 'i' and resid 179 through 192 removed outlier: 3.640A pdb=" N LYS i 190 " --> pdb=" O ARG i 186 " (cutoff:3.500A) Processing helix chain 'i' and resid 193 through 198 removed outlier: 3.575A pdb=" N GLN i 197 " --> pdb=" O PRO i 193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU i 198 " --> pdb=" O LEU i 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 193 through 198' Processing helix chain 'i' and resid 198 through 221 Proline residue: i 210 - end of helix Processing helix chain 'i' and resid 271 through 297 Proline residue: i 278 - end of helix removed outlier: 3.542A pdb=" N ARG i 296 " --> pdb=" O VAL i 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN i 297 " --> pdb=" O CYS i 293 " (cutoff:3.500A) Processing helix chain 'i' and resid 501 through 503 No H-bonds generated for 'chain 'i' and resid 501 through 503' Processing helix chain 'i' and resid 521 through 541 removed outlier: 3.537A pdb=" N PHE i 540 " --> pdb=" O LEU i 536 " (cutoff:3.500A) Processing helix chain 'i' and resid 558 through 573 removed outlier: 4.259A pdb=" N ALA i 567 " --> pdb=" O ALA i 563 " (cutoff:3.500A) Proline residue: i 568 - end of helix Processing helix chain 'i' and resid 584 through 590 Processing helix chain 'i' and resid 591 through 602 Processing helix chain 'i' and resid 604 through 623 removed outlier: 3.793A pdb=" N TYR i 608 " --> pdb=" O ARG i 604 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 44 removed outlier: 3.799A pdb=" N MET j 37 " --> pdb=" O THR j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 54 Processing helix chain 'j' and resid 55 through 60 Processing helix chain 'j' and resid 62 through 80 removed outlier: 3.839A pdb=" N THR j 66 " --> pdb=" O SER j 62 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA j 80 " --> pdb=" O ALA j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 98 Processing helix chain 'j' and resid 100 through 109 Processing helix chain 'j' and resid 112 through 147 Processing helix chain 'j' and resid 156 through 167 Processing helix chain 'j' and resid 179 through 191 removed outlier: 3.517A pdb=" N LYS j 190 " --> pdb=" O ARG j 186 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN j 191 " --> pdb=" O ALA j 187 " (cutoff:3.500A) Processing helix chain 'j' and resid 192 through 197 removed outlier: 3.708A pdb=" N THR j 195 " --> pdb=" O HIS j 192 " (cutoff:3.500A) Processing helix chain 'j' and resid 198 through 221 Proline residue: j 210 - end of helix Processing helix chain 'j' and resid 271 through 296 Proline residue: j 278 - end of helix removed outlier: 3.762A pdb=" N ARG j 296 " --> pdb=" O VAL j 292 " (cutoff:3.500A) Processing helix chain 'j' and resid 521 through 541 Processing helix chain 'j' and resid 558 through 573 removed outlier: 4.285A pdb=" N ALA j 567 " --> pdb=" O ALA j 563 " (cutoff:3.500A) Proline residue: j 568 - end of helix Processing helix chain 'j' and resid 584 through 590 removed outlier: 3.806A pdb=" N VAL j 588 " --> pdb=" O THR j 584 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE j 589 " --> pdb=" O GLY j 585 " (cutoff:3.500A) Processing helix chain 'j' and resid 592 through 602 Processing helix chain 'j' and resid 603 through 623 removed outlier: 3.675A pdb=" N THR j 607 " --> pdb=" O THR j 603 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 45 removed outlier: 3.782A pdb=" N MET k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 54 Processing helix chain 'k' and resid 55 through 60 removed outlier: 3.506A pdb=" N VAL k 59 " --> pdb=" O VAL k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 62 through 79 Processing helix chain 'k' and resid 82 through 98 Processing helix chain 'k' and resid 100 through 109 Processing helix chain 'k' and resid 112 through 147 Processing helix chain 'k' and resid 148 through 150 No H-bonds generated for 'chain 'k' and resid 148 through 150' Processing helix chain 'k' and resid 156 through 167 Processing helix chain 'k' and resid 179 through 192 Processing helix chain 'k' and resid 193 through 198 removed outlier: 3.858A pdb=" N LEU k 198 " --> pdb=" O LEU k 194 " (cutoff:3.500A) Processing helix chain 'k' and resid 198 through 221 Proline residue: k 210 - end of helix Processing helix chain 'k' and resid 271 through 297 Proline residue: k 278 - end of helix removed outlier: 3.558A pdb=" N ASN k 297 " --> pdb=" O CYS k 293 " (cutoff:3.500A) Processing helix chain 'k' and resid 499 through 503 removed outlier: 4.105A pdb=" N SER k 502 " --> pdb=" O VAL k 499 " (cutoff:3.500A) Processing helix chain 'k' and resid 521 through 541 Processing helix chain 'k' and resid 558 through 573 removed outlier: 4.433A pdb=" N ALA k 567 " --> pdb=" O ALA k 563 " (cutoff:3.500A) Proline residue: k 568 - end of helix Processing helix chain 'k' and resid 591 through 603 removed outlier: 3.814A pdb=" N LEU k 595 " --> pdb=" O GLY k 591 " (cutoff:3.500A) Processing helix chain 'k' and resid 604 through 623 removed outlier: 3.701A pdb=" N TYR k 608 " --> pdb=" O ARG k 604 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 44 removed outlier: 3.842A pdb=" N MET l 37 " --> pdb=" O THR l 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 54 Processing helix chain 'l' and resid 55 through 60 Processing helix chain 'l' and resid 62 through 80 removed outlier: 3.880A pdb=" N ALA l 80 " --> pdb=" O ALA l 76 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 98 Processing helix chain 'l' and resid 100 through 109 Processing helix chain 'l' and resid 112 through 147 Processing helix chain 'l' and resid 148 through 150 No H-bonds generated for 'chain 'l' and resid 148 through 150' Processing helix chain 'l' and resid 156 through 167 Processing helix chain 'l' and resid 179 through 190 removed outlier: 4.207A pdb=" N LYS l 190 " --> pdb=" O ARG l 186 " (cutoff:3.500A) Processing helix chain 'l' and resid 192 through 197 removed outlier: 3.516A pdb=" N THR l 195 " --> pdb=" O HIS l 192 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 221 Proline residue: l 210 - end of helix Processing helix chain 'l' and resid 271 through 297 Proline residue: l 278 - end of helix removed outlier: 3.702A pdb=" N ASN l 297 " --> pdb=" O CYS l 293 " (cutoff:3.500A) Processing helix chain 'l' and resid 521 through 541 removed outlier: 3.570A pdb=" N PHE l 540 " --> pdb=" O LEU l 536 " (cutoff:3.500A) Processing helix chain 'l' and resid 558 through 573 removed outlier: 4.197A pdb=" N ALA l 567 " --> pdb=" O ALA l 563 " (cutoff:3.500A) Proline residue: l 568 - end of helix Processing helix chain 'l' and resid 584 through 590 removed outlier: 3.950A pdb=" N VAL l 588 " --> pdb=" O THR l 584 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE l 589 " --> pdb=" O GLY l 585 " (cutoff:3.500A) Processing helix chain 'l' and resid 591 through 602 Processing helix chain 'l' and resid 603 through 623 removed outlier: 3.879A pdb=" N THR l 607 " --> pdb=" O THR l 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 26 through 29 removed outlier: 3.649A pdb=" N ASP a 240 " --> pdb=" O ASN a 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 222 through 224 removed outlier: 3.647A pdb=" N LEU a 255 " --> pdb=" O VAL a 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'a' and resid 495 through 498 removed outlier: 6.527A pdb=" N VAL a 301 " --> pdb=" O ILE a 496 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP a 498 " --> pdb=" O VAL a 301 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL a 303 " --> pdb=" O ASP a 498 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS a 302 " --> pdb=" O SER b 512 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER b 512 " --> pdb=" O LYS a 302 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU a 304 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 508 through 514 removed outlier: 6.759A pdb=" N LEU c 304 " --> pdb=" O ALA a 510 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER a 512 " --> pdb=" O LYS c 302 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS c 302 " --> pdb=" O SER a 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 542 through 544 Processing sheet with id=AA7, first strand: chain 'b' and resid 26 through 29 removed outlier: 3.788A pdb=" N ASP b 240 " --> pdb=" O ASN b 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 222 through 224 Processing sheet with id=AA9, first strand: chain 'b' and resid 261 through 262 Processing sheet with id=AB1, first strand: chain 'b' and resid 495 through 499 removed outlier: 7.054A pdb=" N VAL b 301 " --> pdb=" O ILE b 496 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP b 498 " --> pdb=" O VAL b 301 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL b 303 " --> pdb=" O ASP b 498 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS b 302 " --> pdb=" O SER l 512 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER l 512 " --> pdb=" O LYS b 302 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU b 304 " --> pdb=" O ALA l 510 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR l 508 " --> pdb=" O GLY b 306 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 542 through 546 removed outlier: 3.572A pdb=" N SER b 554 " --> pdb=" O HIS b 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 27 through 29 Processing sheet with id=AB4, first strand: chain 'c' and resid 222 through 224 removed outlier: 3.801A pdb=" N LEU c 255 " --> pdb=" O VAL c 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 261 through 262 Processing sheet with id=AB6, first strand: chain 'c' and resid 509 through 514 removed outlier: 6.726A pdb=" N LEU d 304 " --> pdb=" O ALA c 510 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER c 512 " --> pdb=" O LYS d 302 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS d 302 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL d 301 " --> pdb=" O ILE d 496 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASP d 498 " --> pdb=" O VAL d 301 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL d 303 " --> pdb=" O ASP d 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 542 through 545 removed outlier: 3.857A pdb=" N SER c 554 " --> pdb=" O HIS c 545 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 26 through 29 removed outlier: 3.591A pdb=" N ASN d 235 " --> pdb=" O ASP d 240 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP d 240 " --> pdb=" O ASN d 235 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN d 250 " --> pdb=" O ASP d 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 222 through 224 removed outlier: 3.613A pdb=" N LEU d 255 " --> pdb=" O VAL d 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 261 through 262 Processing sheet with id=AC2, first strand: chain 'd' and resid 509 through 514 removed outlier: 6.811A pdb=" N LEU e 304 " --> pdb=" O ALA d 510 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER d 512 " --> pdb=" O LYS e 302 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS e 302 " --> pdb=" O SER d 512 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL e 301 " --> pdb=" O ILE e 496 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASP e 498 " --> pdb=" O VAL e 301 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL e 303 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 542 through 546 removed outlier: 3.820A pdb=" N SER d 554 " --> pdb=" O HIS d 545 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 27 through 29 removed outlier: 3.664A pdb=" N GLN e 250 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 222 through 224 removed outlier: 3.594A pdb=" N LEU e 255 " --> pdb=" O VAL e 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 261 through 262 Processing sheet with id=AC7, first strand: chain 'e' and resid 507 through 514 removed outlier: 6.952A pdb=" N LEU f 304 " --> pdb=" O ALA e 510 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER e 512 " --> pdb=" O LYS f 302 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS f 302 " --> pdb=" O SER e 512 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL f 301 " --> pdb=" O ILE f 496 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP f 498 " --> pdb=" O VAL f 301 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL f 303 " --> pdb=" O ASP f 498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 542 through 545 removed outlier: 3.721A pdb=" N SER e 554 " --> pdb=" O HIS e 545 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 26 through 29 removed outlier: 3.710A pdb=" N ASP f 240 " --> pdb=" O ASN f 235 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 222 through 224 removed outlier: 3.702A pdb=" N LEU f 255 " --> pdb=" O VAL f 170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 261 through 262 Processing sheet with id=AD3, first strand: chain 'f' and resid 508 through 514 removed outlier: 6.150A pdb=" N VAL f 509 " --> pdb=" O GLY g 306 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY g 306 " --> pdb=" O VAL f 509 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN f 511 " --> pdb=" O LEU g 304 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL g 301 " --> pdb=" O ILE g 496 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ASP g 498 " --> pdb=" O VAL g 301 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL g 303 " --> pdb=" O ASP g 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 544 through 546 removed outlier: 5.142A pdb=" N HIS f 545 " --> pdb=" O THR f 553 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'g' and resid 26 through 29 removed outlier: 3.502A pdb=" N ASN g 235 " --> pdb=" O ASP g 240 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP g 240 " --> pdb=" O ASN g 235 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP g 241 " --> pdb=" O CYS g 254 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS g 254 " --> pdb=" O TRP g 241 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL g 243 " --> pdb=" O GLY g 252 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG g 251 " --> pdb=" O ARG g 174 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARG g 174 " --> pdb=" O ARG g 251 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU g 255 " --> pdb=" O VAL g 170 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'g' and resid 261 through 262 Processing sheet with id=AD7, first strand: chain 'g' and resid 508 through 514 removed outlier: 3.645A pdb=" N TYR g 508 " --> pdb=" O GLY h 306 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU h 304 " --> pdb=" O ALA g 510 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER g 512 " --> pdb=" O LYS h 302 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS h 302 " --> pdb=" O SER g 512 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 542 through 546 removed outlier: 7.383A pdb=" N LEU g 543 " --> pdb=" O ILE g 555 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE g 555 " --> pdb=" O LEU g 543 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS g 545 " --> pdb=" O THR g 553 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 26 through 29 Processing sheet with id=AE1, first strand: chain 'h' and resid 222 through 224 removed outlier: 3.636A pdb=" N LEU h 255 " --> pdb=" O VAL h 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'h' and resid 261 through 262 Processing sheet with id=AE3, first strand: chain 'h' and resid 508 through 514 removed outlier: 6.774A pdb=" N LEU i 304 " --> pdb=" O ALA h 510 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER h 512 " --> pdb=" O LYS i 302 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS i 302 " --> pdb=" O SER h 512 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL i 301 " --> pdb=" O ILE i 496 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP i 498 " --> pdb=" O VAL i 301 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL i 303 " --> pdb=" O ASP i 498 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'h' and resid 542 through 546 removed outlier: 3.537A pdb=" N SER h 554 " --> pdb=" O HIS h 545 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'i' and resid 26 through 29 removed outlier: 3.744A pdb=" N ASP i 240 " --> pdb=" O ASN i 235 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN i 250 " --> pdb=" O ASP i 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'i' and resid 172 through 174 Processing sheet with id=AE7, first strand: chain 'i' and resid 261 through 262 Processing sheet with id=AE8, first strand: chain 'i' and resid 508 through 514 removed outlier: 3.626A pdb=" N TYR i 508 " --> pdb=" O GLY j 306 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU j 304 " --> pdb=" O ALA i 510 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER i 512 " --> pdb=" O LYS j 302 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS j 302 " --> pdb=" O SER i 512 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'i' and resid 542 through 544 Processing sheet with id=AF1, first strand: chain 'j' and resid 26 through 29 removed outlier: 3.841A pdb=" N ASP j 240 " --> pdb=" O ASN j 235 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN j 250 " --> pdb=" O ASP j 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'j' and resid 222 through 224 Processing sheet with id=AF3, first strand: chain 'j' and resid 508 through 514 removed outlier: 6.230A pdb=" N VAL j 509 " --> pdb=" O GLY k 306 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY k 306 " --> pdb=" O VAL j 509 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN j 511 " --> pdb=" O LEU k 304 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL k 301 " --> pdb=" O ILE k 496 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP k 498 " --> pdb=" O VAL k 301 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL k 303 " --> pdb=" O ASP k 498 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'j' and resid 542 through 546 removed outlier: 7.257A pdb=" N LEU j 543 " --> pdb=" O ILE j 555 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE j 555 " --> pdb=" O LEU j 543 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N HIS j 545 " --> pdb=" O THR j 553 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'k' and resid 26 through 29 removed outlier: 3.582A pdb=" N GLN k 250 " --> pdb=" O ASP k 245 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'k' and resid 222 through 224 removed outlier: 3.596A pdb=" N LEU k 255 " --> pdb=" O VAL k 170 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'k' and resid 261 through 262 Processing sheet with id=AF8, first strand: chain 'k' and resid 508 through 514 removed outlier: 3.520A pdb=" N TYR k 508 " --> pdb=" O GLY l 306 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU l 304 " --> pdb=" O ALA k 510 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER k 512 " --> pdb=" O LYS l 302 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS l 302 " --> pdb=" O SER k 512 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL l 301 " --> pdb=" O ILE l 496 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASP l 498 " --> pdb=" O VAL l 301 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL l 303 " --> pdb=" O ASP l 498 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'k' and resid 542 through 544 Processing sheet with id=AG1, first strand: chain 'l' and resid 26 through 29 removed outlier: 3.623A pdb=" N ASP l 240 " --> pdb=" O ASN l 235 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'l' and resid 222 through 224 removed outlier: 3.726A pdb=" N LEU l 255 " --> pdb=" O VAL l 170 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'l' and resid 261 through 262 Processing sheet with id=AG4, first strand: chain 'l' and resid 542 through 546 removed outlier: 4.005A pdb=" N SER l 554 " --> pdb=" O HIS l 545 " (cutoff:3.500A) 2364 hydrogen bonds defined for protein. 6894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.22 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13306 1.34 - 1.46: 8186 1.46 - 1.58: 19020 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 40644 Sorted by residual: bond pdb=" C HIS f 515 " pdb=" O HIS f 515 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.05e-02 9.07e+03 1.46e+00 bond pdb=" C HIS g 515 " pdb=" O HIS g 515 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.05e-02 9.07e+03 1.46e+00 bond pdb=" C HIS j 515 " pdb=" O HIS j 515 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.05e-02 9.07e+03 1.45e+00 bond pdb=" C HIS e 515 " pdb=" O HIS e 515 " ideal model delta sigma weight residual 1.241 1.229 0.012 1.05e-02 9.07e+03 1.41e+00 bond pdb=" C HIS d 515 " pdb=" O HIS d 515 " ideal model delta sigma weight residual 1.241 1.229 0.012 1.05e-02 9.07e+03 1.31e+00 ... (remaining 40639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 55092 3.12 - 6.24: 176 6.24 - 9.35: 8 9.35 - 12.47: 3 12.47 - 15.59: 5 Bond angle restraints: 55284 Sorted by residual: angle pdb=" O HIS i 515 " pdb=" C HIS i 515 " pdb=" N PRO i 516 " ideal model delta sigma weight residual 121.27 106.68 14.59 6.00e-01 2.78e+00 5.91e+02 angle pdb=" O HIS l 515 " pdb=" C HIS l 515 " pdb=" N PRO l 516 " ideal model delta sigma weight residual 121.27 107.23 14.04 6.00e-01 2.78e+00 5.48e+02 angle pdb=" O HIS c 515 " pdb=" C HIS c 515 " pdb=" N PRO c 516 " ideal model delta sigma weight residual 121.23 105.64 15.59 7.00e-01 2.04e+00 4.96e+02 angle pdb=" O HIS f 515 " pdb=" C HIS f 515 " pdb=" N PRO f 516 " ideal model delta sigma weight residual 121.27 108.11 13.16 6.00e-01 2.78e+00 4.81e+02 angle pdb=" O HIS g 515 " pdb=" C HIS g 515 " pdb=" N PRO g 516 " ideal model delta sigma weight residual 121.27 111.76 9.51 6.00e-01 2.78e+00 2.51e+02 ... (remaining 55279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21798 17.90 - 35.81: 1782 35.81 - 53.71: 253 53.71 - 71.61: 67 71.61 - 89.52: 40 Dihedral angle restraints: 23940 sinusoidal: 9564 harmonic: 14376 Sorted by residual: dihedral pdb=" CA GLN d 549 " pdb=" C GLN d 549 " pdb=" N GLY d 550 " pdb=" CA GLY d 550 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TRP j 258 " pdb=" C TRP j 258 " pdb=" N PRO j 259 " pdb=" CA PRO j 259 " ideal model delta harmonic sigma weight residual 180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU i 41 " pdb=" CG GLU i 41 " pdb=" CD GLU i 41 " pdb=" OE1 GLU i 41 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 23937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3707 0.027 - 0.055: 1412 0.055 - 0.082: 528 0.082 - 0.110: 342 0.110 - 0.137: 59 Chirality restraints: 6048 Sorted by residual: chirality pdb=" CA ASP d 125 " pdb=" N ASP d 125 " pdb=" C ASP d 125 " pdb=" CB ASP d 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ASP b 125 " pdb=" N ASP b 125 " pdb=" C ASP b 125 " pdb=" CB ASP b 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ASP l 125 " pdb=" N ASP l 125 " pdb=" C ASP l 125 " pdb=" CB ASP l 125 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 6045 not shown) Planarity restraints: 7176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS c 515 " -0.075 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C HIS c 515 " 0.233 2.00e-02 2.50e+03 pdb=" O HIS c 515 " -0.084 2.00e-02 2.50e+03 pdb=" N PRO c 516 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS i 515 " -0.072 2.00e-02 2.50e+03 1.31e-01 1.71e+02 pdb=" C HIS i 515 " 0.226 2.00e-02 2.50e+03 pdb=" O HIS i 515 " -0.082 2.00e-02 2.50e+03 pdb=" N PRO i 516 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS l 515 " -0.070 2.00e-02 2.50e+03 1.27e-01 1.62e+02 pdb=" C HIS l 515 " 0.220 2.00e-02 2.50e+03 pdb=" O HIS l 515 " -0.080 2.00e-02 2.50e+03 pdb=" N PRO l 516 " -0.070 2.00e-02 2.50e+03 ... (remaining 7173 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 20950 3.01 - 3.48: 41334 3.48 - 3.95: 60294 3.95 - 4.43: 68206 4.43 - 4.90: 110624 Nonbonded interactions: 301408 Sorted by model distance: nonbonded pdb=" O ARG d 122 " pdb=" OD1 ASP d 125 " model vdw 2.533 3.040 nonbonded pdb=" O ARG l 122 " pdb=" OD1 ASP l 125 " model vdw 2.537 3.040 nonbonded pdb=" O ARG b 122 " pdb=" OD1 ASP b 125 " model vdw 2.538 3.040 nonbonded pdb=" O GLU a 594 " pdb=" OD1 ASP a 597 " model vdw 2.540 3.040 nonbonded pdb=" O LYS b 159 " pdb=" OD1 ASP b 162 " model vdw 2.560 3.040 ... (remaining 301403 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: 0.01 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 10.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 38.360 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.003 0.037 40644 Z= 0.127 Angle : 0.517 15.588 55284 Z= 0.363 Chirality : 0.040 0.137 6048 Planarity : 0.006 0.135 7176 Dihedral : 13.559 89.517 14700 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 1.87 (0.12), residues: 4920 helix: 2.65 (0.10), residues: 2772 sheet: 0.04 (0.23), residues: 516 loop : -0.90 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG h 128 TYR 0.012 0.001 TYR h 160 PHE 0.018 0.001 PHE i 157 TRP 0.022 0.001 TRP c 127 HIS 0.006 0.001 HIS l 44 Details of bonding type rmsd covalent geometry : bond 0.00279 (40644) covalent geometry : angle 0.51720 (55284) hydrogen bonds : bond 0.14633 ( 2364) hydrogen bonds : angle 5.36824 ( 6894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 915 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 297 ASN cc_start: 0.8310 (t0) cc_final: 0.7742 (t0) REVERT: a 304 LEU cc_start: 0.9324 (tp) cc_final: 0.9106 (tp) REVERT: a 606 GLN cc_start: 0.8965 (tp40) cc_final: 0.8741 (mm-40) REVERT: b 535 GLU cc_start: 0.7690 (tp30) cc_final: 0.7389 (mm-30) REVERT: c 304 LEU cc_start: 0.9218 (tp) cc_final: 0.8971 (tt) REVERT: c 535 GLU cc_start: 0.7828 (tp30) cc_final: 0.7624 (mm-30) REVERT: e 535 GLU cc_start: 0.8141 (tp30) cc_final: 0.7912 (mm-30) REVERT: f 535 GLU cc_start: 0.7939 (tp30) cc_final: 0.7315 (mm-30) REVERT: g 535 GLU cc_start: 0.7797 (tp30) cc_final: 0.7209 (mm-30) REVERT: h 178 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7737 (mt-10) REVERT: h 604 ARG cc_start: 0.8638 (ptp90) cc_final: 0.8414 (ptm-80) REVERT: i 535 GLU cc_start: 0.7961 (tp30) cc_final: 0.7332 (mm-30) REVERT: j 535 GLU cc_start: 0.7965 (tp30) cc_final: 0.7197 (mm-30) REVERT: j 606 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8469 (tp-100) REVERT: k 297 ASN cc_start: 0.8417 (t0) cc_final: 0.8129 (t0) REVERT: l 125 ASP cc_start: 0.8702 (p0) cc_final: 0.8265 (p0) REVERT: l 162 ASP cc_start: 0.7994 (t0) cc_final: 0.7623 (t0) REVERT: l 535 GLU cc_start: 0.7961 (tp30) cc_final: 0.7527 (mm-30) outliers start: 0 outliers final: 0 residues processed: 915 average time/residue: 0.2701 time to fit residues: 389.6565 Evaluate side-chains 550 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.0570 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 0.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS b 44 HIS b 545 HIS c 511 ASN d 191 GLN e 75 HIS g 289 HIS g 606 GLN h 545 HIS j 515 HIS k 44 HIS k 515 HIS l 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.193599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158521 restraints weight = 55555.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156254 restraints weight = 96889.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157368 restraints weight = 92854.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157203 restraints weight = 53925.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159777 restraints weight = 47450.248| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 40644 Z= 0.166 Angle : 0.570 11.609 55284 Z= 0.297 Chirality : 0.042 0.185 6048 Planarity : 0.004 0.063 7176 Dihedral : 3.739 17.508 5580 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.13 % Allowed : 9.61 % Favored : 88.26 % 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: 1.75 (0.12), residues: 4920 helix: 2.54 (0.10), residues: 2868 sheet: -0.06 (0.23), residues: 516 loop : -1.15 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 604 TYR 0.044 0.002 TYR h 608 PHE 0.015 0.001 PHE b 269 TRP 0.042 0.002 TRP e 127 HIS 0.007 0.001 HIS e 236 Details of bonding type rmsd covalent geometry : bond 0.00397 (40644) covalent geometry : angle 0.57016 (55284) hydrogen bonds : bond 0.04520 ( 2364) hydrogen bonds : angle 4.38530 ( 6894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 575 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 297 ASN cc_start: 0.8343 (t0) cc_final: 0.8029 (t0) REVERT: a 535 GLU cc_start: 0.8120 (tp30) cc_final: 0.7798 (mm-30) REVERT: a 606 GLN cc_start: 0.7815 (tp40) cc_final: 0.7611 (tt0) REVERT: b 535 GLU cc_start: 0.7792 (tp30) cc_final: 0.7224 (mm-30) REVERT: d 75 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: e 297 ASN cc_start: 0.8458 (t0) cc_final: 0.8170 (t0) REVERT: f 214 GLU cc_start: 0.7607 (tp30) cc_final: 0.7342 (tp30) REVERT: f 600 PHE cc_start: 0.6707 (t80) cc_final: 0.6034 (t80) REVERT: h 297 ASN cc_start: 0.8480 (t0) cc_final: 0.8170 (t0) REVERT: h 535 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7861 (tp30) REVERT: i 146 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8289 (t80) REVERT: i 214 GLU cc_start: 0.7566 (tp30) cc_final: 0.7278 (tp30) REVERT: i 535 GLU cc_start: 0.7868 (tp30) cc_final: 0.7404 (mm-30) REVERT: i 583 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7984 (pt) REVERT: k 47 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7912 (pp) REVERT: k 190 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7717 (tmtt) REVERT: l 162 ASP cc_start: 0.8153 (t0) cc_final: 0.7914 (t0) outliers start: 88 outliers final: 62 residues processed: 634 average time/residue: 0.2534 time to fit residues: 259.8385 Evaluate side-chains 563 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 497 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 222 THR Chi-restraints excluded: chain a residue 293 CYS Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain b residue 300 SER Chi-restraints excluded: chain c residue 175 LYS Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 293 CYS Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 511 ASN Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 293 CYS Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 572 SER Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 293 CYS Chi-restraints excluded: chain e residue 494 TYR Chi-restraints excluded: chain f residue 226 ASP Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 293 CYS Chi-restraints excluded: chain f residue 303 VAL Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 605 LEU Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 226 ASP Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 293 CYS Chi-restraints excluded: chain g residue 303 VAL Chi-restraints excluded: chain g residue 494 TYR Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 293 CYS Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain h residue 572 SER Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 292 VAL Chi-restraints excluded: chain i residue 293 CYS Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 572 SER Chi-restraints excluded: chain i residue 583 ILE Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 572 SER Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 293 CYS Chi-restraints excluded: chain k residue 494 TYR Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 226 ASP Chi-restraints excluded: chain l residue 292 VAL Chi-restraints excluded: chain l residue 293 CYS Chi-restraints excluded: chain l residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 368 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 476 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 400 optimal weight: 0.8980 chunk 396 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 370 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 515 HIS c 515 HIS d 606 GLN h 545 HIS i 191 GLN k 297 ASN l 236 HIS l 515 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.193070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157547 restraints weight = 55565.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155820 restraints weight = 100681.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157090 restraints weight = 93119.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157057 restraints weight = 56725.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157649 restraints weight = 53247.993| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40644 Z= 0.145 Angle : 0.544 12.068 55284 Z= 0.283 Chirality : 0.041 0.177 6048 Planarity : 0.004 0.068 7176 Dihedral : 3.674 17.221 5580 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.22 % Allowed : 11.40 % Favored : 86.38 % 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: 1.79 (0.12), residues: 4920 helix: 2.53 (0.10), residues: 2892 sheet: -0.02 (0.24), residues: 528 loop : -1.11 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 604 TYR 0.038 0.001 TYR h 608 PHE 0.012 0.001 PHE f 600 TRP 0.047 0.002 TRP d 127 HIS 0.018 0.001 HIS e 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (40644) covalent geometry : angle 0.54373 (55284) hydrogen bonds : bond 0.04119 ( 2364) hydrogen bonds : angle 4.24455 ( 6894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 523 time to evaluate : 1.519 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 293 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8413 (m) REVERT: a 297 ASN cc_start: 0.8402 (t0) cc_final: 0.8132 (t0) REVERT: a 535 GLU cc_start: 0.8236 (tp30) cc_final: 0.7804 (mm-30) REVERT: b 535 GLU cc_start: 0.7838 (tp30) cc_final: 0.7618 (mm-30) REVERT: d 75 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.8008 (t-90) REVERT: e 100 GLN cc_start: 0.5520 (mp10) cc_final: 0.5187 (mp10) REVERT: e 297 ASN cc_start: 0.8477 (t0) cc_final: 0.8202 (t0) REVERT: e 535 GLU cc_start: 0.8110 (tp30) cc_final: 0.7871 (tp30) REVERT: f 40 ARG cc_start: 0.7950 (tpt-90) cc_final: 0.7709 (tpt-90) REVERT: f 214 GLU cc_start: 0.7487 (tp30) cc_final: 0.7246 (tp30) REVERT: h 293 CYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8296 (m) REVERT: h 297 ASN cc_start: 0.8501 (t0) cc_final: 0.8237 (t0) REVERT: h 608 TYR cc_start: 0.6369 (m-80) cc_final: 0.5526 (m-80) REVERT: i 214 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: i 535 GLU cc_start: 0.7857 (tp30) cc_final: 0.7349 (mm-30) REVERT: j 75 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7810 (t-90) REVERT: k 47 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8001 (pp) REVERT: k 128 ARG cc_start: 0.7501 (ptp-170) cc_final: 0.7285 (ptp-170) REVERT: k 190 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7690 (tmtt) REVERT: k 293 CYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8462 (m) REVERT: l 40 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7344 (tpp80) REVERT: l 162 ASP cc_start: 0.8221 (t0) cc_final: 0.7734 (t0) REVERT: l 557 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8311 (m-10) outliers start: 92 outliers final: 57 residues processed: 584 average time/residue: 0.2571 time to fit residues: 240.9266 Evaluate side-chains 554 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 489 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 293 CYS Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 494 TYR Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 293 CYS Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 293 CYS Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 293 CYS Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 215 LEU Chi-restraints excluded: chain f residue 226 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 293 CYS Chi-restraints excluded: chain f residue 300 SER Chi-restraints excluded: chain g residue 146 PHE Chi-restraints excluded: chain g residue 226 ASP Chi-restraints excluded: chain g residue 293 CYS Chi-restraints excluded: chain g residue 303 VAL Chi-restraints excluded: chain g residue 494 TYR Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 142 LEU Chi-restraints excluded: chain h residue 161 ILE Chi-restraints excluded: chain h residue 293 CYS Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 214 GLU Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 293 CYS Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 496 ILE Chi-restraints excluded: chain j residue 543 LEU Chi-restraints excluded: chain j residue 605 LEU Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 293 CYS Chi-restraints excluded: chain k residue 494 TYR Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 293 CYS Chi-restraints excluded: chain l residue 303 VAL Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 392 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 chunk 449 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 319 optimal weight: 0.4980 chunk 479 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 385 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS b 297 ASN c 511 ASN e 75 HIS ** f 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 545 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.194934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.161454 restraints weight = 55387.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157673 restraints weight = 93879.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158798 restraints weight = 93313.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158602 restraints weight = 56077.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158941 restraints weight = 52954.303| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40644 Z= 0.113 Angle : 0.526 13.010 55284 Z= 0.269 Chirality : 0.040 0.198 6048 Planarity : 0.004 0.046 7176 Dihedral : 3.556 15.556 5580 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.44 % Allowed : 12.44 % Favored : 85.12 % 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: 1.99 (0.13), residues: 4920 helix: 2.71 (0.10), residues: 2844 sheet: 0.06 (0.24), residues: 528 loop : -0.95 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 604 TYR 0.031 0.001 TYR h 608 PHE 0.013 0.001 PHE j 212 TRP 0.058 0.002 TRP d 127 HIS 0.006 0.001 HIS e 236 Details of bonding type rmsd covalent geometry : bond 0.00252 (40644) covalent geometry : angle 0.52570 (55284) hydrogen bonds : bond 0.03641 ( 2364) hydrogen bonds : angle 4.07398 ( 6894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 514 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 293 CYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8352 (m) REVERT: a 535 GLU cc_start: 0.8233 (tp30) cc_final: 0.7705 (tp30) REVERT: d 75 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7971 (t-90) REVERT: e 297 ASN cc_start: 0.8432 (t0) cc_final: 0.8231 (t0) REVERT: f 214 GLU cc_start: 0.7496 (tp30) cc_final: 0.7246 (tp30) REVERT: h 293 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8239 (m) REVERT: i 214 GLU cc_start: 0.7330 (tp30) cc_final: 0.7053 (tp30) REVERT: i 535 GLU cc_start: 0.7781 (tp30) cc_final: 0.7253 (mm-30) REVERT: j 75 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7715 (t-90) REVERT: k 47 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7975 (pp) REVERT: k 128 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.7297 (ptp-170) REVERT: k 190 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7539 (tmtt) REVERT: l 162 ASP cc_start: 0.8106 (t0) cc_final: 0.7899 (t0) REVERT: l 545 HIS cc_start: 0.7107 (m90) cc_final: 0.6772 (m-70) REVERT: l 557 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8280 (m-80) outliers start: 101 outliers final: 68 residues processed: 579 average time/residue: 0.2567 time to fit residues: 240.2294 Evaluate side-chains 558 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 484 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 222 THR Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 293 CYS Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain b residue 605 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 293 CYS Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 511 ASN Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 146 PHE Chi-restraints excluded: chain d residue 200 THR Chi-restraints excluded: chain d residue 293 CYS Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 572 SER Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 293 CYS Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 293 CYS Chi-restraints excluded: chain f residue 300 SER Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain g residue 146 PHE Chi-restraints excluded: chain g residue 214 GLU Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 226 ASP Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 293 CYS Chi-restraints excluded: chain g residue 303 VAL Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 142 LEU Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 293 CYS Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 496 ILE Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 293 CYS Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 146 PHE Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 496 ILE Chi-restraints excluded: chain j residue 605 LEU Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 293 CYS Chi-restraints excluded: chain k residue 494 TYR Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 146 PHE Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 293 CYS Chi-restraints excluded: chain l residue 303 VAL Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 362 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 432 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 405 optimal weight: 3.9990 chunk 458 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 459 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS b 102 GLN b 110 ASN b 274 GLN c 274 GLN d 274 GLN e 75 HIS e 274 GLN f 274 GLN ** f 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 93 HIS ** g 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 274 GLN h 274 GLN h 545 HIS i 274 GLN j 274 GLN k 93 HIS ** k 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 274 GLN l 274 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149174 restraints weight = 56430.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142195 restraints weight = 120811.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134604 restraints weight = 71209.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135099 restraints weight = 71542.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134675 restraints weight = 67696.160| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.081 40644 Z= 0.477 Angle : 0.879 11.504 55284 Z= 0.455 Chirality : 0.052 0.246 6048 Planarity : 0.006 0.098 7176 Dihedral : 4.397 23.539 5580 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 3.89 % Allowed : 14.32 % Favored : 81.79 % 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: 0.97 (0.12), residues: 4920 helix: 1.98 (0.10), residues: 2844 sheet: -0.81 (0.25), residues: 516 loop : -1.40 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG g 186 TYR 0.043 0.003 TYR f 83 PHE 0.025 0.003 PHE a 146 TRP 0.065 0.004 TRP d 127 HIS 0.019 0.002 HIS e 75 Details of bonding type rmsd covalent geometry : bond 0.01173 (40644) covalent geometry : angle 0.87929 (55284) hydrogen bonds : bond 0.06549 ( 2364) hydrogen bonds : angle 5.04146 ( 6894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 493 time to evaluate : 1.346 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 146 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8720 (t80) REVERT: a 517 TYR cc_start: 0.8838 (t80) cc_final: 0.8583 (t80) REVERT: a 535 GLU cc_start: 0.8269 (tp30) cc_final: 0.8026 (tp30) REVERT: a 557 TYR cc_start: 0.9390 (OUTLIER) cc_final: 0.8835 (m-10) REVERT: b 557 TYR cc_start: 0.9478 (OUTLIER) cc_final: 0.9263 (m-10) REVERT: c 557 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: d 75 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.8586 (t-90) REVERT: d 501 LYS cc_start: 0.6839 (mmtt) cc_final: 0.6571 (mmtt) REVERT: d 557 TYR cc_start: 0.9442 (OUTLIER) cc_final: 0.9126 (m-10) REVERT: e 293 CYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8470 (m) REVERT: e 297 ASN cc_start: 0.8595 (t0) cc_final: 0.8315 (t0) REVERT: e 535 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8041 (tp30) REVERT: e 557 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8750 (m-10) REVERT: f 214 GLU cc_start: 0.8395 (tp30) cc_final: 0.8035 (tp30) REVERT: g 100 GLN cc_start: 0.5727 (mp10) cc_final: 0.5189 (mp10) REVERT: h 293 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8427 (m) REVERT: h 535 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7986 (tp30) REVERT: h 557 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.8771 (m-10) REVERT: i 146 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8723 (t80) REVERT: i 214 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: i 557 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8861 (m-10) REVERT: j 75 HIS cc_start: 0.8847 (OUTLIER) cc_final: 0.8230 (t-90) REVERT: j 128 ARG cc_start: 0.8579 (ptp-170) cc_final: 0.8042 (ptp-170) REVERT: j 600 PHE cc_start: 0.8304 (t80) cc_final: 0.8019 (t80) REVERT: k 125 ASP cc_start: 0.8831 (m-30) cc_final: 0.8085 (m-30) REVERT: k 128 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8085 (ptp-170) REVERT: k 557 TYR cc_start: 0.9395 (OUTLIER) cc_final: 0.9080 (m-10) REVERT: l 128 ARG cc_start: 0.8738 (ptp-170) cc_final: 0.8285 (ptp-170) REVERT: l 304 LEU cc_start: 0.9200 (tp) cc_final: 0.8967 (tt) REVERT: l 557 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.8661 (m-80) outliers start: 161 outliers final: 106 residues processed: 607 average time/residue: 0.2517 time to fit residues: 248.3746 Evaluate side-chains 576 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 454 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 146 PHE Chi-restraints excluded: chain a residue 162 ASP Chi-restraints excluded: chain a residue 222 THR Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 293 CYS Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 494 TYR Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain a residue 557 TYR Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 162 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain b residue 300 SER Chi-restraints excluded: chain b residue 303 VAL Chi-restraints excluded: chain b residue 557 TYR Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 162 ASP Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 293 CYS Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 509 VAL Chi-restraints excluded: chain c residue 557 TYR Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 503 MET Chi-restraints excluded: chain d residue 557 TYR Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 293 CYS Chi-restraints excluded: chain e residue 494 TYR Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain e residue 557 TYR Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 215 LEU Chi-restraints excluded: chain f residue 226 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 293 CYS Chi-restraints excluded: chain f residue 300 SER Chi-restraints excluded: chain f residue 494 TYR Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 592 GLU Chi-restraints excluded: chain f residue 607 THR Chi-restraints excluded: chain g residue 214 GLU Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 303 VAL Chi-restraints excluded: chain g residue 494 TYR Chi-restraints excluded: chain g residue 508 TYR Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 142 LEU Chi-restraints excluded: chain h residue 162 ASP Chi-restraints excluded: chain h residue 170 VAL Chi-restraints excluded: chain h residue 226 ASP Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 293 CYS Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 507 THR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain h residue 557 TYR Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 162 ASP Chi-restraints excluded: chain i residue 214 GLU Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 292 VAL Chi-restraints excluded: chain i residue 293 CYS Chi-restraints excluded: chain i residue 494 TYR Chi-restraints excluded: chain i residue 508 TYR Chi-restraints excluded: chain i residue 542 ILE Chi-restraints excluded: chain i residue 557 TYR Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 226 ASP Chi-restraints excluded: chain j residue 292 VAL Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 494 TYR Chi-restraints excluded: chain j residue 503 MET Chi-restraints excluded: chain j residue 543 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 226 ASP Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 293 CYS Chi-restraints excluded: chain k residue 303 VAL Chi-restraints excluded: chain k residue 494 TYR Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain k residue 557 TYR Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 226 ASP Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 292 VAL Chi-restraints excluded: chain l residue 293 CYS Chi-restraints excluded: chain l residue 303 VAL Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 337 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS ** f 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 545 HIS l 511 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.192117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153002 restraints weight = 55507.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150795 restraints weight = 86659.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152326 restraints weight = 85460.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152605 restraints weight = 51548.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153058 restraints weight = 48310.571| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40644 Z= 0.123 Angle : 0.573 10.042 55284 Z= 0.295 Chirality : 0.041 0.255 6048 Planarity : 0.004 0.046 7176 Dihedral : 3.843 17.874 5580 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.25 % Allowed : 16.30 % Favored : 81.45 % 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: 1.55 (0.13), residues: 4920 helix: 2.35 (0.10), residues: 2916 sheet: -0.46 (0.25), residues: 528 loop : -1.14 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 604 TYR 0.034 0.001 TYR f 83 PHE 0.017 0.001 PHE f 157 TRP 0.053 0.002 TRP l 127 HIS 0.018 0.001 HIS e 75 Details of bonding type rmsd covalent geometry : bond 0.00277 (40644) covalent geometry : angle 0.57331 (55284) hydrogen bonds : bond 0.03953 ( 2364) hydrogen bonds : angle 4.31585 ( 6894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 521 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 293 CYS cc_start: 0.8862 (m) cc_final: 0.8392 (m) REVERT: a 535 GLU cc_start: 0.8279 (tp30) cc_final: 0.7804 (tp30) REVERT: d 47 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8926 (pt) REVERT: d 75 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8207 (t-90) REVERT: e 40 ARG cc_start: 0.8014 (tpt90) cc_final: 0.7751 (tpt90) REVERT: e 297 ASN cc_start: 0.8489 (t0) cc_final: 0.8219 (t0) REVERT: f 214 GLU cc_start: 0.7672 (tp30) cc_final: 0.7317 (tp30) REVERT: g 557 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8998 (m-10) REVERT: g 604 ARG cc_start: 0.6338 (ttp80) cc_final: 0.5848 (ttp80) REVERT: h 253 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6478 (pt0) REVERT: i 214 GLU cc_start: 0.7628 (tp30) cc_final: 0.7287 (tp30) REVERT: j 75 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7900 (t-90) REVERT: j 511 ASN cc_start: 0.8569 (t0) cc_final: 0.8114 (m-40) REVERT: k 47 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7913 (pp) REVERT: k 190 LYS cc_start: 0.8044 (tmtt) cc_final: 0.7792 (tmtt) REVERT: l 557 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8367 (m-80) outliers start: 93 outliers final: 65 residues processed: 582 average time/residue: 0.2635 time to fit residues: 244.6103 Evaluate side-chains 560 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 488 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain a residue 605 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 169 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 542 ILE Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 36 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 146 PHE Chi-restraints excluded: chain d residue 253 GLU Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 542 ILE Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 501 LYS Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 607 THR Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 303 VAL Chi-restraints excluded: chain g residue 557 TYR Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 161 ILE Chi-restraints excluded: chain h residue 253 GLU Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 507 THR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 36 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 271 SER Chi-restraints excluded: chain l residue 511 ASN Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 433 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 chunk 481 optimal weight: 4.9990 chunk 352 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 361 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS d 545 HIS e 75 HIS f 511 ASN g 297 ASN h 545 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.191444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156363 restraints weight = 55533.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154334 restraints weight = 100140.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155303 restraints weight = 99081.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155367 restraints weight = 59422.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155678 restraints weight = 55290.689| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40644 Z= 0.147 Angle : 0.582 10.211 55284 Z= 0.299 Chirality : 0.042 0.255 6048 Planarity : 0.004 0.046 7176 Dihedral : 3.728 17.023 5580 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.75 % Allowed : 16.67 % Favored : 80.58 % 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: 1.68 (0.13), residues: 4920 helix: 2.49 (0.10), residues: 2856 sheet: -0.40 (0.25), residues: 528 loop : -1.04 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 604 TYR 0.028 0.001 TYR b 508 PHE 0.016 0.001 PHE f 600 TRP 0.037 0.002 TRP d 127 HIS 0.006 0.001 HIS e 236 Details of bonding type rmsd covalent geometry : bond 0.00349 (40644) covalent geometry : angle 0.58200 (55284) hydrogen bonds : bond 0.04120 ( 2364) hydrogen bonds : angle 4.28112 ( 6894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 504 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 535 GLU cc_start: 0.8244 (tp30) cc_final: 0.7747 (tp30) REVERT: a 557 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: c 125 ASP cc_start: 0.6686 (t0) cc_final: 0.6392 (t0) REVERT: d 47 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8950 (pt) REVERT: d 75 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.8033 (t-90) REVERT: d 557 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: e 100 GLN cc_start: 0.6201 (mp10) cc_final: 0.5979 (mp10) REVERT: e 297 ASN cc_start: 0.8519 (t0) cc_final: 0.8277 (t0) REVERT: e 535 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7844 (tp30) REVERT: g 100 GLN cc_start: 0.5264 (mp10) cc_final: 0.5050 (mp10) REVERT: g 557 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8909 (m-10) REVERT: h 557 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: i 214 GLU cc_start: 0.7368 (tp30) cc_final: 0.7040 (tp30) REVERT: j 75 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7839 (t-90) REVERT: j 511 ASN cc_start: 0.8497 (t0) cc_final: 0.8072 (m-40) REVERT: j 557 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8951 (m-10) REVERT: k 47 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8120 (pp) REVERT: k 190 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7629 (tmtt) REVERT: l 545 HIS cc_start: 0.7037 (m90) cc_final: 0.6814 (m90) REVERT: l 557 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8405 (m-80) outliers start: 114 outliers final: 86 residues processed: 582 average time/residue: 0.2553 time to fit residues: 238.0681 Evaluate side-chains 577 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 481 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 146 PHE Chi-restraints excluded: chain a residue 222 THR Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain a residue 557 TYR Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 169 LEU Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain b residue 303 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 240 ASP Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 300 SER Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 36 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 75 HIS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 300 SER Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 542 ILE Chi-restraints excluded: chain d residue 557 TYR Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 501 LYS Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 226 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 293 CYS Chi-restraints excluded: chain f residue 303 VAL Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 607 THR Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 303 VAL Chi-restraints excluded: chain g residue 509 VAL Chi-restraints excluded: chain g residue 557 TYR Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 146 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 507 THR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain h residue 557 TYR Chi-restraints excluded: chain i residue 36 THR Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 293 CYS Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 36 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 301 VAL Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 557 TYR Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 293 CYS Chi-restraints excluded: chain l residue 303 VAL Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 436 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 449 optimal weight: 0.9990 chunk 396 optimal weight: 0.0470 chunk 368 optimal weight: 9.9990 chunk 317 optimal weight: 0.0050 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS ** e 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 515 HIS g 545 HIS h 545 HIS l 511 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.194416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160487 restraints weight = 55299.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157701 restraints weight = 98756.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.158490 restraints weight = 96337.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158103 restraints weight = 57829.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158531 restraints weight = 54937.972| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 40644 Z= 0.113 Angle : 0.555 10.888 55284 Z= 0.282 Chirality : 0.041 0.273 6048 Planarity : 0.004 0.049 7176 Dihedral : 3.537 14.613 5580 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.27 % Allowed : 17.15 % Favored : 80.58 % 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: 1.83 (0.13), residues: 4920 helix: 2.57 (0.10), residues: 2856 sheet: -0.16 (0.25), residues: 528 loop : -0.96 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG c 128 TYR 0.028 0.001 TYR b 508 PHE 0.016 0.001 PHE f 600 TRP 0.033 0.002 TRP d 127 HIS 0.010 0.001 HIS l 236 Details of bonding type rmsd covalent geometry : bond 0.00250 (40644) covalent geometry : angle 0.55496 (55284) hydrogen bonds : bond 0.03456 ( 2364) hydrogen bonds : angle 4.08535 ( 6894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 515 time to evaluate : 1.568 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 125 ASP cc_start: 0.6465 (t0) cc_final: 0.6126 (t0) REVERT: a 535 GLU cc_start: 0.8232 (tp30) cc_final: 0.7722 (tp30) REVERT: d 47 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8854 (pt) REVERT: e 535 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7740 (tp30) REVERT: h 297 ASN cc_start: 0.8565 (t0) cc_final: 0.8311 (t0) REVERT: i 214 GLU cc_start: 0.7231 (tp30) cc_final: 0.6913 (tp30) REVERT: j 75 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: j 511 ASN cc_start: 0.8498 (t0) cc_final: 0.8125 (m-40) REVERT: j 557 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8784 (m-10) REVERT: k 47 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7850 (pp) REVERT: k 190 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7629 (tmtt) REVERT: l 545 HIS cc_start: 0.6962 (m90) cc_final: 0.6637 (m90) outliers start: 94 outliers final: 73 residues processed: 581 average time/residue: 0.2556 time to fit residues: 237.7367 Evaluate side-chains 549 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 472 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 146 PHE Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 509 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain a residue 605 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 303 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 146 PHE Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 253 GLU Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 497 ILE Chi-restraints excluded: chain d residue 542 ILE Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 605 LEU Chi-restraints excluded: chain f residue 607 THR Chi-restraints excluded: chain g residue 146 PHE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 226 ASP Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 509 VAL Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 146 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 507 THR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 494 TYR Chi-restraints excluded: chain j residue 557 TYR Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 511 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 336 optimal weight: 0.0470 chunk 195 optimal weight: 0.4980 chunk 166 optimal weight: 0.5980 chunk 332 optimal weight: 0.9990 chunk 345 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 360 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 545 HIS l 511 ASN l 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158638 restraints weight = 55599.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154766 restraints weight = 102112.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.156466 restraints weight = 92364.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156320 restraints weight = 55124.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159432 restraints weight = 48240.973| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40644 Z= 0.114 Angle : 0.574 11.640 55284 Z= 0.289 Chirality : 0.041 0.275 6048 Planarity : 0.004 0.045 7176 Dihedral : 3.486 14.631 5580 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.22 % Allowed : 17.58 % Favored : 80.19 % 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: 1.89 (0.13), residues: 4920 helix: 2.57 (0.10), residues: 2892 sheet: -0.08 (0.25), residues: 528 loop : -0.93 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 128 TYR 0.028 0.001 TYR g 608 PHE 0.020 0.001 PHE j 124 TRP 0.057 0.002 TRP i 90 HIS 0.004 0.001 HIS d 545 Details of bonding type rmsd covalent geometry : bond 0.00257 (40644) covalent geometry : angle 0.57362 (55284) hydrogen bonds : bond 0.03476 ( 2364) hydrogen bonds : angle 4.04751 ( 6894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 489 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 535 GLU cc_start: 0.8266 (tp30) cc_final: 0.7766 (tp30) REVERT: d 47 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8842 (pt) REVERT: e 535 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7704 (tp30) REVERT: g 604 ARG cc_start: 0.5715 (ttp80) cc_final: 0.5144 (ttp80) REVERT: i 214 GLU cc_start: 0.7420 (tp30) cc_final: 0.7084 (tp30) REVERT: j 75 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7916 (t-90) REVERT: j 511 ASN cc_start: 0.8612 (t0) cc_final: 0.8222 (m-40) REVERT: j 557 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8758 (m-10) REVERT: k 47 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7922 (pp) REVERT: l 190 LYS cc_start: 0.7078 (pptt) cc_final: 0.6732 (pttp) REVERT: l 545 HIS cc_start: 0.6860 (m90) cc_final: 0.6644 (m90) REVERT: l 557 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8358 (m-10) outliers start: 92 outliers final: 78 residues processed: 551 average time/residue: 0.2596 time to fit residues: 228.5694 Evaluate side-chains 556 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 473 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 HIS Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 146 PHE Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 509 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain a residue 605 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain b residue 303 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 293 CYS Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 253 GLU Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 542 ILE Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 511 ASN Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 605 LEU Chi-restraints excluded: chain f residue 607 THR Chi-restraints excluded: chain g residue 146 PHE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 226 ASP Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 509 VAL Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 161 ILE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 507 THR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 36 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 494 TYR Chi-restraints excluded: chain j residue 557 TYR Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 511 ASN Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 167 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 404 optimal weight: 0.0980 chunk 360 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 470 optimal weight: 0.6980 chunk 418 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 370 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.194753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158449 restraints weight = 55236.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154754 restraints weight = 102492.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156478 restraints weight = 90208.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156271 restraints weight = 57453.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156853 restraints weight = 52943.199| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40644 Z= 0.114 Angle : 0.583 12.013 55284 Z= 0.293 Chirality : 0.041 0.286 6048 Planarity : 0.004 0.048 7176 Dihedral : 3.436 14.257 5580 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.13 % Allowed : 17.85 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.13), residues: 4920 helix: 2.56 (0.10), residues: 2892 sheet: -0.07 (0.25), residues: 528 loop : -0.91 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 604 TYR 0.033 0.001 TYR j 608 PHE 0.029 0.001 PHE h 138 TRP 0.053 0.002 TRP i 90 HIS 0.003 0.000 HIS d 545 Details of bonding type rmsd covalent geometry : bond 0.00258 (40644) covalent geometry : angle 0.58307 (55284) hydrogen bonds : bond 0.03421 ( 2364) hydrogen bonds : angle 4.01210 ( 6894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 488 time to evaluate : 1.603 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: a 535 GLU cc_start: 0.8197 (tp30) cc_final: 0.7700 (tp30) REVERT: d 47 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8802 (pt) REVERT: e 535 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7664 (tp30) REVERT: i 214 GLU cc_start: 0.7336 (tp30) cc_final: 0.7024 (tp30) REVERT: j 75 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7818 (t-90) REVERT: j 511 ASN cc_start: 0.8539 (t0) cc_final: 0.8187 (m-40) REVERT: j 557 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8734 (m-10) REVERT: k 47 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7922 (pp) REVERT: l 190 LYS cc_start: 0.7012 (pptt) cc_final: 0.6618 (ptmm) REVERT: l 545 HIS cc_start: 0.6895 (m90) cc_final: 0.6665 (m90) REVERT: l 557 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8370 (m-10) outliers start: 88 outliers final: 81 residues processed: 549 average time/residue: 0.2674 time to fit residues: 235.5482 Evaluate side-chains 551 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 465 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 HIS Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 146 PHE Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 256 VAL Chi-restraints excluded: chain a residue 303 VAL Chi-restraints excluded: chain a residue 494 TYR Chi-restraints excluded: chain a residue 509 VAL Chi-restraints excluded: chain a residue 542 ILE Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 293 CYS Chi-restraints excluded: chain b residue 303 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 215 LEU Chi-restraints excluded: chain c residue 222 THR Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 303 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 253 GLU Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 301 VAL Chi-restraints excluded: chain d residue 303 VAL Chi-restraints excluded: chain d residue 494 TYR Chi-restraints excluded: chain d residue 542 ILE Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 146 PHE Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 303 VAL Chi-restraints excluded: chain e residue 496 ILE Chi-restraints excluded: chain e residue 501 LYS Chi-restraints excluded: chain e residue 511 ASN Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 293 CYS Chi-restraints excluded: chain f residue 511 ASN Chi-restraints excluded: chain f residue 557 TYR Chi-restraints excluded: chain f residue 605 LEU Chi-restraints excluded: chain f residue 607 THR Chi-restraints excluded: chain g residue 146 PHE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 226 ASP Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 509 VAL Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 161 ILE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 303 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 542 ILE Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 146 PHE Chi-restraints excluded: chain i residue 161 ILE Chi-restraints excluded: chain i residue 215 LEU Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 605 LEU Chi-restraints excluded: chain j residue 36 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 75 HIS Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 300 SER Chi-restraints excluded: chain j residue 303 VAL Chi-restraints excluded: chain j residue 494 TYR Chi-restraints excluded: chain j residue 496 ILE Chi-restraints excluded: chain j residue 557 TYR Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 182 THR Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 293 CYS Chi-restraints excluded: chain k residue 503 MET Chi-restraints excluded: chain l residue 215 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 557 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 122 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 253 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 394 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.194535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.161049 restraints weight = 55595.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157516 restraints weight = 93492.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158405 restraints weight = 96397.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158479 restraints weight = 54912.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160631 restraints weight = 47115.281| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40644 Z= 0.120 Angle : 0.597 11.304 55284 Z= 0.301 Chirality : 0.041 0.277 6048 Planarity : 0.004 0.049 7176 Dihedral : 3.440 17.080 5580 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.25 % Allowed : 18.12 % Favored : 79.64 % 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: 1.87 (0.13), residues: 4920 helix: 2.52 (0.10), residues: 2892 sheet: 0.05 (0.25), residues: 516 loop : -0.92 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG e 128 TYR 0.047 0.001 TYR j 608 PHE 0.018 0.001 PHE h 138 TRP 0.051 0.002 TRP i 90 HIS 0.004 0.001 HIS d 545 Details of bonding type rmsd covalent geometry : bond 0.00276 (40644) covalent geometry : angle 0.59690 (55284) hydrogen bonds : bond 0.03499 ( 2364) hydrogen bonds : angle 4.01136 ( 6894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6322.58 seconds wall clock time: 110 minutes 6.91 seconds (6606.91 seconds total)