Starting phenix.real_space_refine on Tue Aug 26 19:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9op4_70678/08_2025/9op4_70678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9op4_70678/08_2025/9op4_70678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9op4_70678/08_2025/9op4_70678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9op4_70678/08_2025/9op4_70678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9op4_70678/08_2025/9op4_70678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9op4_70678/08_2025/9op4_70678.map" } resolution = 3.6 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= 0.057 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 25776 2.51 5 N 7296 2.21 5 O 7296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40476 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "a" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "b" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "c" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "d" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "e" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "f" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "g" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "h" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "i" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "j" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "k" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Chain: "l" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3317 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain breaks: 1 Time building chain proxies: 8.74, per 1000 atoms: 0.22 Number of scatterers: 40476 At special positions: 0 Unit cell: (160.6, 158.4, 157.3, 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 7296 8.00 N 7296 7.00 C 25776 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 476.8 nanoseconds 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9432 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 53 sheets defined 63.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'a' and resid 33 through 45 removed outlier: 3.670A 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: 3.760A pdb=" N VAL a 59 " --> pdb=" O VAL a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 80 removed outlier: 3.564A pdb=" N ALA a 80 " --> pdb=" O ALA a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 98 removed outlier: 3.528A pdb=" N LEU a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 109 Processing helix chain 'a' and resid 112 through 147 removed outlier: 4.339A pdb=" N CYS a 145 " --> pdb=" O GLY a 141 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE a 146 " --> pdb=" O LEU a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 150 No H-bonds generated for 'chain 'a' and resid 148 through 150' Processing helix chain 'a' and resid 156 through 167 Processing helix chain 'a' and resid 179 through 192 removed outlier: 3.684A pdb=" N LYS a 190 " --> pdb=" O ARG a 186 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN a 191 " --> pdb=" O ALA a 187 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS a 192 " --> pdb=" O PHE a 188 " (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: 3.533A pdb=" N LEU a 295 " --> pdb=" O HIS a 291 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG a 296 " --> pdb=" O VAL a 292 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN a 297 " --> pdb=" O CYS a 293 " (cutoff:3.500A) Processing helix chain 'a' and resid 501 through 504 removed outlier: 3.636A pdb=" N ASP a 504 " --> pdb=" O LYS a 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 501 through 504' Processing helix chain 'a' and resid 521 through 541 Processing helix chain 'a' and resid 558 through 573 removed outlier: 3.972A pdb=" N ALA a 567 " --> pdb=" O ALA a 563 " (cutoff:3.500A) Proline residue: a 568 - end of helix Processing helix chain 'a' and resid 585 through 590 removed outlier: 4.259A pdb=" N ILE a 589 " --> pdb=" O GLY a 585 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU a 590 " --> pdb=" O SER a 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 585 through 590' Processing helix chain 'a' and resid 591 through 602 Processing helix chain 'a' and resid 603 through 623 removed outlier: 3.940A pdb=" N THR a 607 " --> pdb=" O THR a 603 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 44 removed outlier: 3.518A pdb=" N MET b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG b 40 " --> pdb=" O THR b 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 54 Processing helix chain 'b' and resid 55 through 60 removed outlier: 3.609A pdb=" N VAL b 59 " --> pdb=" O VAL b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 80 removed outlier: 3.515A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 98 removed outlier: 3.615A pdb=" N LEU b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 109 Processing helix chain 'b' and resid 112 through 147 removed outlier: 3.535A pdb=" N ILE b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS b 145 " --> pdb=" O GLY b 141 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE b 146 " --> pdb=" O LEU b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 150 No H-bonds generated for 'chain 'b' and resid 148 through 150' Processing helix chain 'b' and resid 156 through 167 Processing helix chain 'b' and resid 179 through 190 Processing helix chain 'b' and resid 192 through 198 removed outlier: 4.022A pdb=" N ARG b 196 " --> pdb=" O HIS b 192 " (cutoff:3.500A) 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: 3.920A pdb=" N ALA b 282 " --> pdb=" O PRO b 278 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU b 295 " --> pdb=" O HIS b 291 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG b 296 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN b 297 " --> pdb=" O CYS b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 521 through 540 Processing helix chain 'b' and resid 558 through 572 removed outlier: 3.891A pdb=" N ALA b 567 " --> pdb=" O ALA b 563 " (cutoff:3.500A) Proline residue: b 568 - end of helix Processing helix chain 'b' and resid 584 through 589 removed outlier: 3.530A pdb=" N VAL b 588 " --> pdb=" O GLY b 585 " (cutoff:3.500A) Processing helix chain 'b' and resid 591 through 602 removed outlier: 3.611A pdb=" N LYS b 602 " --> pdb=" O ALA b 598 " (cutoff:3.500A) Processing helix chain 'b' and resid 603 through 623 removed outlier: 3.762A pdb=" N THR b 607 " --> pdb=" O THR b 603 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 44 removed outlier: 3.744A pdb=" N MET c 37 " --> pdb=" O THR c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 54 Processing helix chain 'c' and resid 55 through 60 removed outlier: 3.799A pdb=" N VAL c 59 " --> pdb=" O VAL c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 80 removed outlier: 3.613A pdb=" N ALA c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 98 removed outlier: 3.509A pdb=" N LEU c 86 " --> pdb=" O THR c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 109 Processing helix chain 'c' and resid 112 through 144 Processing helix chain 'c' and resid 145 through 150 Proline residue: c 148 - end of helix No H-bonds generated for 'chain 'c' and resid 145 through 150' Processing helix chain 'c' and resid 156 through 167 removed outlier: 3.623A pdb=" N TYR c 160 " --> pdb=" O SER c 156 " (cutoff:3.500A) Processing helix chain 'c' and resid 179 through 190 Processing helix chain 'c' and resid 192 through 198 removed outlier: 4.362A pdb=" N ARG c 196 " --> pdb=" O HIS c 192 " (cutoff:3.500A) 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: 3.582A pdb=" N ASN c 297 " --> pdb=" O CYS c 293 " (cutoff:3.500A) Processing helix chain 'c' and resid 501 through 504 removed outlier: 3.803A pdb=" N ASP c 504 " --> pdb=" O LYS c 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 501 through 504' Processing helix chain 'c' and resid 521 through 541 Processing helix chain 'c' and resid 558 through 573 removed outlier: 3.898A pdb=" N ALA c 567 " --> pdb=" O ALA c 563 " (cutoff:3.500A) Proline residue: c 568 - end of helix Processing helix chain 'c' and resid 591 through 602 removed outlier: 3.869A pdb=" N LYS c 602 " --> pdb=" O ALA c 598 " (cutoff:3.500A) Processing helix chain 'c' and resid 603 through 623 removed outlier: 3.730A pdb=" N THR c 607 " --> pdb=" O THR c 603 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 44 removed outlier: 3.541A pdb=" N MET d 37 " --> pdb=" O THR d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 54 Processing helix chain 'd' and resid 55 through 60 removed outlier: 3.645A pdb=" N VAL d 59 " --> pdb=" O VAL d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 81 removed outlier: 3.834A pdb=" N THR d 81 " --> pdb=" O LEU d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 98 removed outlier: 3.643A pdb=" N LEU d 86 " --> pdb=" O THR d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 109 Processing helix chain 'd' and resid 112 through 147 removed outlier: 4.172A pdb=" N CYS d 145 " --> pdb=" O GLY d 141 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE d 146 " --> pdb=" O LEU d 142 " (cutoff:3.500A) 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 190 removed outlier: 3.508A pdb=" N LYS d 190 " --> pdb=" O ARG d 186 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 198 removed outlier: 4.006A 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: 3.936A pdb=" N ALA d 282 " --> pdb=" O PRO d 278 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN d 297 " --> pdb=" O CYS d 293 " (cutoff:3.500A) Processing helix chain 'd' and resid 500 through 504 Processing helix chain 'd' and resid 521 through 541 Processing helix chain 'd' and resid 558 through 572 removed outlier: 3.959A pdb=" N ALA d 567 " --> pdb=" O ALA d 563 " (cutoff:3.500A) Proline residue: d 568 - end of helix Processing helix chain 'd' and resid 584 through 590 removed outlier: 3.755A pdb=" N VAL d 588 " --> pdb=" O THR d 584 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE d 589 " --> pdb=" O GLY d 585 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU d 590 " --> pdb=" O SER d 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 584 through 590' Processing helix chain 'd' and resid 591 through 603 removed outlier: 3.610A pdb=" N LYS d 602 " --> pdb=" O ALA d 598 " (cutoff:3.500A) Processing helix chain 'd' and resid 603 through 623 removed outlier: 4.470A pdb=" N THR d 607 " --> pdb=" O THR d 603 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR d 608 " --> pdb=" O ARG d 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 44 removed outlier: 3.516A pdb=" N ARG e 40 " --> pdb=" O THR e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 54 No H-bonds generated for 'chain 'e' and resid 52 through 54' Processing helix chain 'e' and resid 55 through 60 removed outlier: 3.754A pdb=" N VAL e 59 " --> pdb=" O VAL e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 62 through 81 removed outlier: 4.072A pdb=" N THR e 81 " --> pdb=" O LEU e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 98 removed outlier: 3.624A pdb=" N LEU e 86 " --> pdb=" O THR e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 109 Processing helix chain 'e' and resid 112 through 147 removed outlier: 4.343A pdb=" N CYS e 145 " --> pdb=" O GLY e 141 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE e 146 " --> pdb=" O LEU e 142 " (cutoff:3.500A) 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 removed outlier: 3.525A pdb=" N TYR e 160 " --> pdb=" O SER e 156 " (cutoff:3.500A) Processing helix chain 'e' and resid 179 through 192 removed outlier: 3.619A pdb=" N GLN e 191 " --> pdb=" O ALA e 187 " (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: 3.508A pdb=" N ARG e 296 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN e 297 " --> pdb=" O CYS e 293 " (cutoff:3.500A) Processing helix chain 'e' and resid 500 through 504 removed outlier: 3.866A pdb=" N MET e 503 " --> pdb=" O SER e 500 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 540 Processing helix chain 'e' and resid 558 through 572 removed outlier: 3.966A pdb=" N ALA e 567 " --> pdb=" O ALA e 563 " (cutoff:3.500A) Proline residue: e 568 - end of helix Processing helix chain 'e' and resid 585 through 589 Processing helix chain 'e' and resid 591 through 602 removed outlier: 3.860A pdb=" N LYS e 602 " --> pdb=" O ALA e 598 " (cutoff:3.500A) Processing helix chain 'e' and resid 603 through 623 removed outlier: 3.693A pdb=" N THR e 607 " --> pdb=" O THR e 603 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 44 removed outlier: 3.657A pdb=" N MET f 37 " --> pdb=" O THR f 33 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS f 44 " --> pdb=" O ARG f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 54 Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.624A pdb=" N VAL f 59 " --> pdb=" O VAL f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 62 through 80 removed outlier: 3.553A pdb=" N ALA f 80 " --> pdb=" O ALA f 76 " (cutoff:3.500A) 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 removed outlier: 3.510A pdb=" N ILE f 116 " --> pdb=" O ARG f 112 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS f 145 " --> pdb=" O GLY f 141 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE f 146 " --> pdb=" O LEU f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 156 through 167 Processing helix chain 'f' and resid 179 through 190 removed outlier: 3.745A pdb=" N LYS f 190 " --> pdb=" O ARG f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 192 through 198 removed outlier: 4.190A pdb=" N ARG f 196 " --> pdb=" O HIS f 192 " (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: 3.582A pdb=" N ASN f 297 " --> pdb=" O CYS f 293 " (cutoff:3.500A) Processing helix chain 'f' and resid 500 through 504 Processing helix chain 'f' and resid 521 through 541 Processing helix chain 'f' and resid 558 through 572 removed outlier: 3.993A pdb=" N ALA f 567 " --> pdb=" O ALA f 563 " (cutoff:3.500A) Proline residue: f 568 - end of helix Processing helix chain 'f' and resid 585 through 589 Processing helix chain 'f' and resid 591 through 603 Processing helix chain 'f' and resid 603 through 623 removed outlier: 3.866A pdb=" N THR f 607 " --> pdb=" O THR f 603 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 44 removed outlier: 3.626A 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 61 removed outlier: 3.716A pdb=" N VAL g 59 " --> pdb=" O VAL g 55 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER g 61 " --> pdb=" O ASN g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 80 removed outlier: 3.724A 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 144 Processing helix chain 'g' and resid 145 through 150 Proline residue: g 148 - end of helix No H-bonds generated for 'chain 'g' and resid 145 through 150' Processing helix chain 'g' and resid 156 through 167 Processing helix chain 'g' and resid 179 through 190 Processing helix chain 'g' and resid 192 through 198 removed outlier: 3.831A pdb=" N ARG g 196 " --> pdb=" O HIS g 192 " (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: 3.804A pdb=" N ALA g 282 " --> pdb=" O PRO g 278 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG g 296 " --> pdb=" O VAL g 292 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN g 297 " --> pdb=" O CYS g 293 " (cutoff:3.500A) Processing helix chain 'g' and resid 521 through 540 Processing helix chain 'g' and resid 558 through 573 removed outlier: 3.977A pdb=" N ALA g 567 " --> pdb=" O ALA g 563 " (cutoff:3.500A) Proline residue: g 568 - end of helix Processing helix chain 'g' and resid 584 through 588 Processing helix chain 'g' and resid 591 through 602 Processing helix chain 'g' and resid 603 through 623 removed outlier: 4.007A pdb=" N THR g 607 " --> pdb=" O THR g 603 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 44 removed outlier: 3.736A pdb=" N MET h 37 " --> pdb=" O THR h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 54 Processing helix chain 'h' and resid 55 through 60 removed outlier: 3.702A pdb=" N VAL h 59 " --> pdb=" O VAL h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 81 removed outlier: 3.635A pdb=" N ALA h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR h 81 " --> pdb=" O LEU h 77 " (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 removed outlier: 4.205A pdb=" N CYS h 145 " --> pdb=" O GLY h 141 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE h 146 " --> pdb=" O LEU h 142 " (cutoff:3.500A) 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 Processing helix chain 'h' and resid 179 through 192 removed outlier: 3.674A pdb=" N GLN h 191 " --> pdb=" O ALA h 187 " (cutoff:3.500A) Processing helix chain 'h' and resid 193 through 198 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: 3.519A pdb=" N ARG h 296 " --> pdb=" O VAL h 292 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN h 297 " --> pdb=" O CYS h 293 " (cutoff:3.500A) Processing helix chain 'h' and resid 499 through 504 removed outlier: 3.622A pdb=" N SER h 502 " --> pdb=" O VAL h 499 " (cutoff:3.500A) Processing helix chain 'h' and resid 521 through 540 Processing helix chain 'h' and resid 558 through 573 removed outlier: 3.983A pdb=" N ALA h 567 " --> pdb=" O ALA h 563 " (cutoff:3.500A) Proline residue: h 568 - end of helix Processing helix chain 'h' and resid 584 through 588 removed outlier: 3.608A pdb=" N VAL h 588 " --> pdb=" O GLY h 585 " (cutoff:3.500A) Processing helix chain 'h' and resid 591 through 602 removed outlier: 3.801A pdb=" N LYS h 602 " --> pdb=" O ALA h 598 " (cutoff:3.500A) Processing helix chain 'h' and resid 603 through 623 removed outlier: 3.723A pdb=" N THR h 607 " --> pdb=" O THR h 603 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 44 removed outlier: 3.698A 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 61 removed outlier: 3.843A pdb=" N VAL i 59 " --> pdb=" O VAL i 55 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER i 61 " --> pdb=" O ASN i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 62 through 80 removed outlier: 3.960A 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 144 Processing helix chain 'i' and resid 145 through 150 Proline residue: i 148 - end of helix No H-bonds generated for 'chain 'i' and resid 145 through 150' Processing helix chain 'i' and resid 156 through 167 Processing helix chain 'i' and resid 179 through 190 removed outlier: 3.540A pdb=" N LYS i 190 " --> pdb=" O ARG i 186 " (cutoff:3.500A) Processing helix chain 'i' and resid 192 through 198 removed outlier: 4.261A pdb=" N ARG i 196 " --> pdb=" O HIS i 192 " (cutoff:3.500A) 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: 3.629A pdb=" N ASN i 297 " --> pdb=" O CYS i 293 " (cutoff:3.500A) Processing helix chain 'i' and resid 521 through 540 Processing helix chain 'i' and resid 558 through 572 removed outlier: 3.852A 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 585 through 590 removed outlier: 4.252A pdb=" N ILE i 589 " --> pdb=" O GLY i 585 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU i 590 " --> pdb=" O SER i 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 585 through 590' Processing helix chain 'i' and resid 591 through 602 removed outlier: 3.686A pdb=" N LYS i 602 " --> pdb=" O ALA i 598 " (cutoff:3.500A) Processing helix chain 'i' and resid 603 through 623 removed outlier: 3.643A pdb=" N THR i 607 " --> pdb=" O THR i 603 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 44 Processing helix chain 'j' and resid 51 through 54 Processing helix chain 'j' and resid 55 through 60 removed outlier: 3.750A pdb=" N VAL j 59 " --> pdb=" O VAL j 55 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 80 removed outlier: 3.671A pdb=" N ALA j 80 " --> pdb=" O ALA j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 98 removed outlier: 3.586A pdb=" N LEU j 86 " --> pdb=" O THR j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 109 Processing helix chain 'j' and resid 112 through 147 removed outlier: 4.249A pdb=" N CYS j 145 " --> pdb=" O GLY j 141 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE j 146 " --> pdb=" O LEU j 142 " (cutoff:3.500A) Processing helix chain 'j' and resid 156 through 167 Processing helix chain 'j' and resid 179 through 190 Processing helix chain 'j' and resid 192 through 198 removed outlier: 4.025A pdb=" N ARG j 196 " --> 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 297 Proline residue: j 278 - end of helix removed outlier: 3.840A pdb=" N ALA j 282 " --> pdb=" O PRO j 278 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG j 296 " --> pdb=" O VAL j 292 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN j 297 " --> pdb=" O CYS j 293 " (cutoff:3.500A) Processing helix chain 'j' and resid 521 through 540 Processing helix chain 'j' and resid 558 through 573 removed outlier: 3.848A 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: 3.798A pdb=" N VAL j 588 " --> pdb=" O GLY j 585 " (cutoff:3.500A) Processing helix chain 'j' and resid 591 through 602 removed outlier: 3.781A pdb=" N LYS j 602 " --> pdb=" O ALA j 598 " (cutoff:3.500A) Processing helix chain 'j' and resid 603 through 623 removed outlier: 3.680A pdb=" N THR j 607 " --> pdb=" O THR j 603 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.740A pdb=" N MET k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 54 Processing helix chain 'k' and resid 55 through 60 removed outlier: 3.627A pdb=" N VAL k 59 " --> pdb=" O VAL k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 62 through 80 removed outlier: 4.015A pdb=" N ALA k 80 " --> pdb=" O ALA k 76 " (cutoff:3.500A) 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 145 removed outlier: 3.594A pdb=" N ILE k 116 " --> pdb=" O ARG k 112 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS k 145 " --> pdb=" O GLY k 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 150 Processing helix chain 'k' and resid 156 through 167 Processing helix chain 'k' and resid 179 through 190 Processing helix chain 'k' and resid 192 through 198 removed outlier: 4.360A pdb=" N ARG k 196 " --> pdb=" O HIS k 192 " (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: 3.764A pdb=" N ALA k 282 " --> pdb=" O PRO k 278 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG k 296 " --> pdb=" O VAL k 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN k 297 " --> pdb=" O CYS k 293 " (cutoff:3.500A) Processing helix chain 'k' and resid 500 through 504 Processing helix chain 'k' and resid 521 through 540 Processing helix chain 'k' and resid 558 through 573 removed outlier: 3.883A 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 584 through 590 Processing helix chain 'k' and resid 591 through 602 removed outlier: 4.008A pdb=" N LYS k 602 " --> pdb=" O ALA k 598 " (cutoff:3.500A) Processing helix chain 'k' and resid 603 through 623 removed outlier: 3.547A pdb=" N THR k 607 " --> pdb=" O THR k 603 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 44 removed outlier: 3.520A 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 removed outlier: 3.664A pdb=" N VAL l 59 " --> pdb=" O VAL l 55 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG l 60 " --> pdb=" O TYR l 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 55 through 60' Processing helix chain 'l' and resid 62 through 80 removed outlier: 3.781A 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 removed outlier: 4.294A pdb=" N CYS l 145 " --> pdb=" O GLY l 141 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE l 146 " --> pdb=" O LEU l 142 " (cutoff:3.500A) Processing helix chain 'l' and resid 156 through 167 Processing helix chain 'l' and resid 179 through 190 Processing helix chain 'l' and resid 192 through 198 removed outlier: 4.067A pdb=" N ARG l 196 " --> 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: 3.894A pdb=" N ALA l 282 " --> pdb=" O PRO l 278 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU l 295 " --> pdb=" O HIS l 291 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN l 297 " --> pdb=" O CYS l 293 " (cutoff:3.500A) Processing helix chain 'l' and resid 501 through 504 Processing helix chain 'l' and resid 521 through 540 Processing helix chain 'l' and resid 558 through 573 removed outlier: 3.907A 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: 3.620A pdb=" N VAL l 588 " --> pdb=" O THR l 584 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE l 589 " --> pdb=" O GLY l 585 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU l 590 " --> pdb=" O SER l 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 584 through 590' Processing helix chain 'l' and resid 591 through 602 removed outlier: 3.837A pdb=" N LYS l 602 " --> pdb=" O ALA l 598 " (cutoff:3.500A) Processing helix chain 'l' and resid 603 through 623 removed outlier: 3.641A 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: 3.503A pdb=" N ASP a 240 " --> pdb=" O ASN a 235 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TRP a 241 " --> pdb=" O CYS a 254 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS a 254 " --> pdb=" O TRP a 241 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL a 243 " --> pdb=" O GLY a 252 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ARG a 251 " --> pdb=" O ARG a 174 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG a 174 " --> pdb=" O ARG a 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 261 through 262 Processing sheet with id=AA3, first strand: chain 'a' and resid 496 through 499 removed outlier: 6.720A pdb=" N LYS a 302 " --> pdb=" O SER b 512 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER b 512 " --> pdb=" O LYS a 302 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU a 304 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 507 through 514 removed outlier: 6.852A pdb=" N LEU c 304 " --> pdb=" O ALA a 510 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER a 512 " --> pdb=" O LYS c 302 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS c 302 " --> pdb=" O SER a 512 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL c 301 " --> pdb=" O ILE c 496 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP c 498 " --> pdb=" O VAL c 301 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL c 303 " --> pdb=" O ASP c 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 542 through 545 removed outlier: 3.841A pdb=" N SER a 554 " --> pdb=" O HIS a 545 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 27 through 29 Processing sheet with id=AA7, first strand: chain 'b' and resid 172 through 174 Processing sheet with id=AA8, first strand: chain 'b' and resid 495 through 498 removed outlier: 6.375A pdb=" N VAL b 301 " --> pdb=" O ILE b 496 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP b 498 " --> pdb=" O VAL b 301 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL b 303 " --> pdb=" O ASP b 498 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS b 302 " --> pdb=" O SER l 512 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER l 512 " --> pdb=" O LYS b 302 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU b 304 " --> pdb=" O ALA l 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 542 through 545 removed outlier: 3.988A pdb=" N SER b 554 " --> pdb=" O HIS b 545 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 27 through 29 Processing sheet with id=AB2, first strand: chain 'c' and resid 222 through 224 Processing sheet with id=AB3, first strand: chain 'c' and resid 507 through 514 removed outlier: 6.735A pdb=" N LEU d 304 " --> pdb=" O ALA c 510 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER c 512 " --> pdb=" O LYS d 302 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS d 302 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL d 301 " --> pdb=" O ILE d 496 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP d 498 " --> pdb=" O VAL d 301 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL d 303 " --> pdb=" O ASP d 498 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 542 through 545 removed outlier: 3.966A pdb=" N SER c 554 " --> pdb=" O HIS c 545 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 26 through 29 Processing sheet with id=AB6, first strand: chain 'd' and resid 172 through 174 Processing sheet with id=AB7, first strand: chain 'd' and resid 507 through 514 removed outlier: 6.883A pdb=" N LEU e 304 " --> pdb=" O ALA d 510 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER d 512 " --> pdb=" O LYS e 302 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS e 302 " --> pdb=" O SER d 512 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL e 301 " --> pdb=" O ILE e 496 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ASP e 498 " --> pdb=" O VAL e 301 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL e 303 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 542 through 545 removed outlier: 3.963A pdb=" N SER d 554 " --> pdb=" O HIS d 545 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 27 through 29 removed outlier: 3.721A pdb=" N ASN e 235 " --> pdb=" O ASP e 240 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP e 240 " --> pdb=" O ASN e 235 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 222 through 224 Processing sheet with id=AC2, first strand: chain 'e' and resid 507 through 514 removed outlier: 6.780A pdb=" N LEU f 304 " --> pdb=" O ALA e 510 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER e 512 " --> pdb=" O LYS f 302 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS f 302 " --> pdb=" O SER e 512 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL f 301 " --> pdb=" O ILE f 496 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ASP f 498 " --> pdb=" O VAL f 301 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL f 303 " --> pdb=" O ASP f 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 542 through 545 removed outlier: 3.953A pdb=" N SER e 554 " --> pdb=" O HIS e 545 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AC5, first strand: chain 'f' and resid 222 through 224 removed outlier: 3.619A pdb=" N LEU f 255 " --> pdb=" O VAL f 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 261 through 262 Processing sheet with id=AC7, first strand: chain 'f' and resid 507 through 514 removed outlier: 6.692A pdb=" N LEU g 304 " --> pdb=" O ALA f 510 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER f 512 " --> pdb=" O LYS g 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS g 302 " --> pdb=" O SER f 512 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL g 301 " --> pdb=" O ILE g 496 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP g 498 " --> pdb=" O VAL g 301 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL g 303 " --> pdb=" O ASP g 498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 542 through 545 removed outlier: 3.992A pdb=" N SER f 554 " --> pdb=" O HIS f 545 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 26 through 29 removed outlier: 3.805A pdb=" N ASN g 235 " --> pdb=" O ASP g 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP g 240 " --> pdb=" O ASN g 235 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 172 through 174 Processing sheet with id=AD2, first strand: chain 'g' and resid 261 through 262 Processing sheet with id=AD3, first strand: chain 'g' and resid 507 through 514 removed outlier: 6.856A pdb=" N LEU h 304 " --> pdb=" O ALA g 510 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER g 512 " --> pdb=" O LYS h 302 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS h 302 " --> pdb=" O SER g 512 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 542 through 545 removed outlier: 3.829A pdb=" N SER g 554 " --> pdb=" O HIS g 545 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'h' and resid 27 through 29 Processing sheet with id=AD6, first strand: chain 'h' and resid 222 through 224 Processing sheet with id=AD7, first strand: chain 'h' and resid 261 through 262 Processing sheet with id=AD8, first strand: chain 'h' and resid 507 through 514 removed outlier: 6.943A pdb=" N LEU i 304 " --> pdb=" O ALA h 510 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER h 512 " --> pdb=" O LYS i 302 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS i 302 " --> pdb=" O SER h 512 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL i 301 " --> pdb=" O ILE i 496 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP i 498 " --> pdb=" O VAL i 301 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL i 303 " --> pdb=" O ASP i 498 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 542 through 545 removed outlier: 4.070A pdb=" N SER h 554 " --> pdb=" O HIS h 545 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'i' and resid 27 through 29 removed outlier: 3.725A pdb=" N ASN i 235 " --> pdb=" O ASP i 240 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP i 240 " --> pdb=" O ASN i 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'i' and resid 222 through 224 removed outlier: 3.618A pdb=" N LEU i 255 " --> pdb=" O VAL i 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'i' and resid 261 through 262 Processing sheet with id=AE4, first strand: chain 'i' and resid 507 through 514 removed outlier: 6.902A pdb=" N LEU j 304 " --> pdb=" O ALA i 510 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER i 512 " --> pdb=" O LYS j 302 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS j 302 " --> pdb=" O SER i 512 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL j 301 " --> pdb=" O ILE j 496 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ASP j 498 " --> pdb=" O VAL j 301 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL j 303 " --> pdb=" O ASP j 498 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'i' and resid 542 through 545 removed outlier: 3.898A pdb=" N SER i 554 " --> pdb=" O HIS i 545 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'j' and resid 26 through 29 Processing sheet with id=AE7, first strand: chain 'j' and resid 222 through 224 removed outlier: 3.527A pdb=" N LEU j 255 " --> pdb=" O VAL j 170 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'j' and resid 507 through 514 removed outlier: 6.764A pdb=" N LEU k 304 " --> pdb=" O ALA j 510 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER j 512 " --> pdb=" O LYS k 302 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS k 302 " --> pdb=" O SER j 512 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL k 301 " --> pdb=" O ILE k 496 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASP k 498 " --> pdb=" O VAL k 301 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL k 303 " --> pdb=" O ASP k 498 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 542 through 545 removed outlier: 3.837A pdb=" N SER j 554 " --> pdb=" O HIS j 545 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'k' and resid 26 through 29 Processing sheet with id=AF2, first strand: chain 'k' and resid 222 through 224 Processing sheet with id=AF3, first strand: chain 'k' and resid 507 through 514 removed outlier: 6.948A pdb=" N LEU l 304 " --> pdb=" O ALA k 510 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER k 512 " --> pdb=" O LYS l 302 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS l 302 " --> pdb=" O SER k 512 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL l 301 " --> pdb=" O ILE l 496 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP l 498 " --> pdb=" O VAL l 301 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL l 303 " --> pdb=" O ASP l 498 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'k' and resid 542 through 545 removed outlier: 4.016A pdb=" N SER k 554 " --> pdb=" O HIS k 545 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'l' and resid 27 through 29 Processing sheet with id=AF6, first strand: chain 'l' and resid 222 through 224 Processing sheet with id=AF7, first strand: chain 'l' and resid 261 through 262 Processing sheet with id=AF8, first strand: chain 'l' and resid 542 through 545 removed outlier: 3.965A pdb=" N SER l 554 " --> pdb=" O HIS l 545 " (cutoff:3.500A) 2315 hydrogen bonds defined for protein. 6696 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: 11.33 Time building geometry restraints manager: 4.27 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: 13558 1.34 - 1.46: 8488 1.46 - 1.57: 19342 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 41520 Sorted by residual: bond pdb=" N ASP d 24 " pdb=" CA ASP d 24 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N ASP k 24 " pdb=" CA ASP k 24 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ASP f 24 " pdb=" CA ASP f 24 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N ASP g 24 " pdb=" CA ASP g 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASP i 24 " pdb=" CA ASP i 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 41515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 54954 1.48 - 2.96: 1230 2.96 - 4.44: 252 4.44 - 5.92: 31 5.92 - 7.40: 5 Bond angle restraints: 56472 Sorted by residual: angle pdb=" N VAL k 579 " pdb=" CA VAL k 579 " pdb=" C VAL k 579 " ideal model delta sigma weight residual 113.20 110.13 3.07 9.60e-01 1.09e+00 1.03e+01 angle pdb=" N VAL l 579 " pdb=" CA VAL l 579 " pdb=" C VAL l 579 " ideal model delta sigma weight residual 113.20 110.16 3.04 9.60e-01 1.09e+00 1.00e+01 angle pdb=" N VAL a 579 " pdb=" CA VAL a 579 " pdb=" C VAL a 579 " ideal model delta sigma weight residual 113.20 110.17 3.03 9.60e-01 1.09e+00 9.99e+00 angle pdb=" C GLU i 178 " pdb=" N GLY i 179 " pdb=" CA GLY i 179 " ideal model delta sigma weight residual 122.16 119.80 2.36 7.70e-01 1.69e+00 9.42e+00 angle pdb=" N VAL j 579 " pdb=" CA VAL j 579 " pdb=" C VAL j 579 " ideal model delta sigma weight residual 113.20 110.27 2.93 9.60e-01 1.09e+00 9.33e+00 ... (remaining 56467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 22532 17.50 - 35.00: 1604 35.00 - 52.50: 241 52.50 - 70.00: 31 70.00 - 87.50: 36 Dihedral angle restraints: 24444 sinusoidal: 9756 harmonic: 14688 Sorted by residual: dihedral pdb=" CA ARG c 266 " pdb=" C ARG c 266 " pdb=" N LEU c 267 " pdb=" CA LEU c 267 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA LEU j 189 " pdb=" C LEU j 189 " pdb=" N LYS j 190 " pdb=" CA LYS j 190 " ideal model delta harmonic sigma weight residual -180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LYS e 501 " pdb=" C LYS e 501 " pdb=" N SER e 502 " pdb=" CA SER e 502 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 24441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3612 0.026 - 0.051: 1525 0.051 - 0.077: 581 0.077 - 0.102: 246 0.102 - 0.128: 180 Chirality restraints: 6144 Sorted by residual: chirality pdb=" CA ILE l 518 " pdb=" N ILE l 518 " pdb=" C ILE l 518 " pdb=" CB ILE l 518 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA VAL d 303 " pdb=" N VAL d 303 " pdb=" C VAL d 303 " pdb=" CB VAL d 303 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA PRO f 34 " pdb=" N PRO f 34 " pdb=" C PRO f 34 " pdb=" CB PRO f 34 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 6141 not shown) Planarity restraints: 7332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE g 219 " 0.018 2.00e-02 2.50e+03 1.91e-02 6.42e+00 pdb=" CG PHE g 219 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE g 219 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE g 219 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE g 219 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE g 219 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE g 219 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE b 219 " -0.016 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE b 219 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE b 219 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE b 219 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE b 219 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE b 219 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE b 219 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE k 219 " -0.013 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE k 219 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE k 219 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE k 219 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE k 219 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE k 219 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE k 219 " -0.005 2.00e-02 2.50e+03 ... (remaining 7329 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 12418 2.84 - 3.35: 39757 3.35 - 3.87: 62408 3.87 - 4.38: 69386 4.38 - 4.90: 121664 Nonbonded interactions: 305633 Sorted by model distance: nonbonded pdb=" O ASP k 505 " pdb=" OD1 ASP k 506 " model vdw 2.321 3.040 nonbonded pdb=" O LYS i 159 " pdb=" OD1 ASP i 162 " model vdw 2.352 3.040 nonbonded pdb=" O LYS g 159 " pdb=" OD1 ASP g 162 " model vdw 2.393 3.040 nonbonded pdb=" O LYS k 159 " pdb=" OD1 ASP k 162 " model vdw 2.393 3.040 nonbonded pdb=" O PHE l 616 " pdb=" OD1 ASP l 619 " model vdw 2.394 3.040 ... (remaining 305628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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' } 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: 9.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.760 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 0.045 41520 Z= 0.152 Angle : 0.568 7.404 56472 Z= 0.323 Chirality : 0.039 0.128 6144 Planarity : 0.004 0.043 7332 Dihedral : 12.588 87.504 15012 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 aren not related in a simple way. whole: 1.09 (0.12), residues: 5004 helix: 2.11 (0.10), residues: 2760 sheet: -0.26 (0.23), residues: 516 loop : -1.30 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 40 TYR 0.014 0.001 TYR e 227 PHE 0.044 0.001 PHE g 219 TRP 0.017 0.001 TRP l 163 HIS 0.005 0.001 HIS c 31 Details of bonding type rmsd covalent geometry : bond 0.00320 (41520) covalent geometry : angle 0.56787 (56472) hydrogen bonds : bond 0.15601 ( 2315) hydrogen bonds : angle 5.70214 ( 6696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 821 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 37 MET cc_start: 0.8832 (mmt) cc_final: 0.8326 (mmt) REVERT: a 236 HIS cc_start: 0.7121 (t70) cc_final: 0.6914 (t70) REVERT: a 517 TYR cc_start: 0.7979 (t80) cc_final: 0.7661 (t80) REVERT: b 250 GLN cc_start: 0.6332 (tt0) cc_final: 0.6122 (tp40) REVERT: b 608 TYR cc_start: 0.7566 (m-10) cc_final: 0.7286 (m-80) REVERT: c 79 ASN cc_start: 0.7992 (t0) cc_final: 0.7646 (t0) REVERT: c 124 PHE cc_start: 0.8431 (t80) cc_final: 0.8167 (t80) REVERT: c 237 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7073 (mmp-170) REVERT: d 182 THR cc_start: 0.8647 (p) cc_final: 0.8435 (t) REVERT: d 592 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8063 (tm-30) REVERT: e 37 MET cc_start: 0.8951 (mmt) cc_final: 0.8421 (mmt) REVERT: e 132 ARG cc_start: 0.7672 (ttt-90) cc_final: 0.6842 (ttt-90) REVERT: f 185 LEU cc_start: 0.8612 (mt) cc_final: 0.8380 (tt) REVERT: f 556 SER cc_start: 0.8668 (p) cc_final: 0.8270 (m) REVERT: g 505 ASP cc_start: 0.8075 (t0) cc_final: 0.7825 (t0) REVERT: g 506 ASP cc_start: 0.7860 (t0) cc_final: 0.7591 (t0) REVERT: g 612 ILE cc_start: 0.8656 (mt) cc_final: 0.8441 (tp) REVERT: h 127 TRP cc_start: 0.8194 (t60) cc_final: 0.7877 (t60) REVERT: h 497 ILE cc_start: 0.8974 (pt) cc_final: 0.8674 (pt) REVERT: h 615 LEU cc_start: 0.8224 (mt) cc_final: 0.7944 (mp) REVERT: i 79 ASN cc_start: 0.7364 (t0) cc_final: 0.7124 (t0) REVERT: i 584 THR cc_start: 0.9241 (m) cc_final: 0.8934 (p) REVERT: j 245 ASP cc_start: 0.7535 (t0) cc_final: 0.7078 (p0) REVERT: j 541 LYS cc_start: 0.7812 (mttt) cc_final: 0.7388 (mttm) REVERT: j 584 THR cc_start: 0.8746 (m) cc_final: 0.8520 (p) REVERT: k 37 MET cc_start: 0.8554 (mmm) cc_final: 0.7765 (mmt) REVERT: k 90 TRP cc_start: 0.7041 (t-100) cc_final: 0.6834 (t-100) REVERT: k 136 LEU cc_start: 0.7925 (tp) cc_final: 0.7451 (tp) REVERT: k 543 LEU cc_start: 0.7950 (tt) cc_final: 0.7600 (pp) REVERT: l 192 HIS cc_start: 0.6893 (t-90) cc_final: 0.6623 (t-90) outliers start: 0 outliers final: 0 residues processed: 821 average time/residue: 0.2465 time to fit residues: 310.5704 Evaluate side-chains 510 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 31 HIS a 57 ASN b 110 ASN b 235 ASN c 57 ASN c 235 ASN c 545 HIS e 57 ASN e 140 HIS e 606 GLN f 57 ASN f 192 HIS f 235 ASN g 57 ASN i 140 HIS j 545 HIS j 621 GLN k 57 ASN k 235 ASN k 545 HIS ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 57 ASN l 545 HIS l 551 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.179215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138357 restraints weight = 53745.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135022 restraints weight = 83038.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137333 restraints weight = 73704.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137323 restraints weight = 44294.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137686 restraints weight = 44596.831| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41520 Z= 0.180 Angle : 0.617 9.134 56472 Z= 0.327 Chirality : 0.043 0.198 6144 Planarity : 0.005 0.042 7332 Dihedral : 4.684 26.495 5700 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.49 % Allowed : 7.13 % Favored : 91.38 % 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 aren not related in a simple way. whole: 1.33 (0.12), residues: 5004 helix: 2.26 (0.10), residues: 2820 sheet: 0.03 (0.24), residues: 492 loop : -1.29 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 237 TYR 0.022 0.002 TYR d 608 PHE 0.029 0.002 PHE e 188 TRP 0.036 0.002 TRP a 127 HIS 0.009 0.001 HIS k 93 Details of bonding type rmsd covalent geometry : bond 0.00428 (41520) covalent geometry : angle 0.61697 (56472) hydrogen bonds : bond 0.05776 ( 2315) hydrogen bonds : angle 4.47610 ( 6696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 532 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 517 TYR cc_start: 0.8019 (t80) cc_final: 0.7745 (t80) REVERT: a 523 GLN cc_start: 0.7295 (mp10) cc_final: 0.6984 (mp10) REVERT: a 543 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7098 (tp) REVERT: b 608 TYR cc_start: 0.7840 (m-10) cc_final: 0.7228 (m-80) REVERT: c 79 ASN cc_start: 0.7764 (t0) cc_final: 0.7375 (t0) REVERT: c 237 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7162 (mmp-170) REVERT: d 592 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8015 (tm-30) REVERT: f 185 LEU cc_start: 0.8602 (mt) cc_final: 0.8394 (tt) REVERT: f 556 SER cc_start: 0.8551 (p) cc_final: 0.8047 (m) REVERT: g 506 ASP cc_start: 0.7758 (t0) cc_final: 0.7555 (t0) REVERT: h 127 TRP cc_start: 0.8312 (t60) cc_final: 0.8035 (t60) REVERT: h 592 GLU cc_start: 0.7694 (tp30) cc_final: 0.7010 (tt0) REVERT: h 615 LEU cc_start: 0.8098 (mt) cc_final: 0.7883 (mm) REVERT: i 255 LEU cc_start: 0.8701 (tp) cc_final: 0.8494 (tt) REVERT: i 584 THR cc_start: 0.9251 (m) cc_final: 0.9011 (p) REVERT: j 136 LEU cc_start: 0.8118 (tp) cc_final: 0.7849 (tt) REVERT: j 541 LYS cc_start: 0.7923 (mttt) cc_final: 0.7626 (mttm) REVERT: k 136 LEU cc_start: 0.8150 (tp) cc_final: 0.7612 (tp) outliers start: 63 outliers final: 43 residues processed: 566 average time/residue: 0.2357 time to fit residues: 211.7881 Evaluate side-chains 507 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 463 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 498 ASP Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 543 LEU Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 191 GLN Chi-restraints excluded: chain b residue 496 ILE Chi-restraints excluded: chain b residue 537 VAL Chi-restraints excluded: chain b residue 607 THR Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 185 LEU Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain e residue 584 THR Chi-restraints excluded: chain e residue 606 GLN Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 506 ASP Chi-restraints excluded: chain h residue 589 ILE Chi-restraints excluded: chain i residue 43 LEU Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 590 LEU Chi-restraints excluded: chain l residue 43 LEU Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 310 ASP Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 558 SER Chi-restraints excluded: chain l residue 588 VAL Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.0170 chunk 159 optimal weight: 3.9990 chunk 478 optimal weight: 1.9990 chunk 403 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 65 optimal weight: 0.0570 chunk 264 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 57 ASN a 197 GLN b 235 ASN c 57 ASN d 235 ASN d 606 GLN d 621 GLN e 57 ASN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 606 GLN g 545 HIS h 177 GLN ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 57 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.182042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138195 restraints weight = 53278.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135344 restraints weight = 60421.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137258 restraints weight = 58444.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137819 restraints weight = 37027.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138299 restraints weight = 32336.444| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 41520 Z= 0.116 Angle : 0.529 7.451 56472 Z= 0.280 Chirality : 0.040 0.142 6144 Planarity : 0.004 0.038 7332 Dihedral : 4.319 27.467 5700 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 9.19 % Favored : 89.61 % 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 aren not related in a simple way. whole: 1.69 (0.12), residues: 5004 helix: 2.54 (0.10), residues: 2820 sheet: 0.25 (0.23), residues: 492 loop : -1.16 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 307 TYR 0.031 0.001 TYR i 608 PHE 0.030 0.001 PHE e 188 TRP 0.017 0.001 TRP a 127 HIS 0.011 0.001 HIS a 236 Details of bonding type rmsd covalent geometry : bond 0.00237 (41520) covalent geometry : angle 0.52893 (56472) hydrogen bonds : bond 0.04545 ( 2315) hydrogen bonds : angle 4.08161 ( 6696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 516 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 517 TYR cc_start: 0.8026 (t80) cc_final: 0.7740 (t80) REVERT: a 602 LYS cc_start: 0.8368 (ptpp) cc_final: 0.7987 (tttt) REVERT: b 506 ASP cc_start: 0.6182 (t0) cc_final: 0.5843 (t0) REVERT: b 608 TYR cc_start: 0.7767 (m-10) cc_final: 0.7240 (m-80) REVERT: c 125 ASP cc_start: 0.8477 (p0) cc_final: 0.8254 (p0) REVERT: c 237 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7103 (mmp-170) REVERT: d 592 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7787 (tm-30) REVERT: e 47 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8351 (pp) REVERT: f 185 LEU cc_start: 0.8695 (mt) cc_final: 0.8362 (tt) REVERT: g 234 TYR cc_start: 0.7881 (t80) cc_final: 0.7585 (t80) REVERT: h 47 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7810 (pp) REVERT: h 127 TRP cc_start: 0.8186 (t60) cc_final: 0.7834 (t60) REVERT: h 496 ILE cc_start: 0.8400 (mt) cc_final: 0.8168 (mt) REVERT: h 592 GLU cc_start: 0.7560 (tp30) cc_final: 0.6898 (tt0) REVERT: h 615 LEU cc_start: 0.8208 (mt) cc_final: 0.7978 (mm) REVERT: i 584 THR cc_start: 0.9201 (m) cc_final: 0.8858 (p) REVERT: j 136 LEU cc_start: 0.8080 (tp) cc_final: 0.7841 (tt) REVERT: j 541 LYS cc_start: 0.7689 (mttt) cc_final: 0.7399 (mttm) REVERT: k 136 LEU cc_start: 0.8084 (tp) cc_final: 0.7381 (tp) REVERT: l 69 LEU cc_start: 0.8073 (tp) cc_final: 0.7857 (tp) outliers start: 51 outliers final: 28 residues processed: 548 average time/residue: 0.2267 time to fit residues: 200.8057 Evaluate side-chains 491 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 461 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 155 SER Chi-restraints excluded: chain b residue 191 GLN Chi-restraints excluded: chain c residue 497 ILE Chi-restraints excluded: chain c residue 571 GLU Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 501 LYS Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 142 LEU Chi-restraints excluded: chain l residue 43 LEU Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 589 ILE Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 304 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 486 optimal weight: 10.0000 chunk 343 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 462 optimal weight: 6.9990 chunk 435 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 461 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 235 ASN d 606 GLN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 606 GLN f 57 ASN i 622 HIS ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 31 HIS l 57 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.176822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136682 restraints weight = 53522.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133467 restraints weight = 87631.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134993 restraints weight = 74231.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136323 restraints weight = 47997.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136405 restraints weight = 43950.704| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 41520 Z= 0.187 Angle : 0.590 11.809 56472 Z= 0.309 Chirality : 0.042 0.157 6144 Planarity : 0.005 0.068 7332 Dihedral : 4.407 28.267 5700 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.20 % Allowed : 9.71 % Favored : 88.09 % 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 aren not related in a simple way. whole: 1.47 (0.12), residues: 5004 helix: 2.37 (0.10), residues: 2820 sheet: 0.20 (0.23), residues: 492 loop : -1.28 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 237 TYR 0.040 0.002 TYR i 608 PHE 0.026 0.002 PHE h 188 TRP 0.014 0.002 TRP b 127 HIS 0.012 0.001 HIS d 93 Details of bonding type rmsd covalent geometry : bond 0.00458 (41520) covalent geometry : angle 0.58997 (56472) hydrogen bonds : bond 0.05186 ( 2315) hydrogen bonds : angle 4.13350 ( 6696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 476 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 602 LYS cc_start: 0.8285 (ptpp) cc_final: 0.7879 (tttt) REVERT: a 615 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7327 (mt) REVERT: b 608 TYR cc_start: 0.7665 (m-10) cc_final: 0.7177 (m-80) REVERT: c 237 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7159 (mmp-170) REVERT: c 594 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7115 (tp30) REVERT: d 592 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7911 (tm-30) REVERT: e 47 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8516 (pp) REVERT: h 127 TRP cc_start: 0.8239 (t60) cc_final: 0.7963 (t60) REVERT: j 541 LYS cc_start: 0.7911 (mttt) cc_final: 0.7545 (mttm) REVERT: j 594 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: k 136 LEU cc_start: 0.8273 (tp) cc_final: 0.6945 (tp) REVERT: k 219 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: l 47 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8229 (pt) outliers start: 93 outliers final: 71 residues processed: 539 average time/residue: 0.2330 time to fit residues: 203.4975 Evaluate side-chains 517 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 441 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 192 HIS Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 155 SER Chi-restraints excluded: chain b residue 191 GLN Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 496 ILE Chi-restraints excluded: chain b residue 537 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 497 ILE Chi-restraints excluded: chain c residue 571 GLU Chi-restraints excluded: chain c residue 589 ILE Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 219 PHE Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 131 LEU Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 253 GLU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain f residue 572 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 78 LEU Chi-restraints excluded: chain g residue 166 CYS Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 507 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 501 LYS Chi-restraints excluded: chain i residue 43 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 255 LEU Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 256 VAL Chi-restraints excluded: chain j residue 594 GLU Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 142 LEU Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 304 LEU Chi-restraints excluded: chain l residue 43 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 310 ASP Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 558 SER Chi-restraints excluded: chain l residue 589 ILE Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 242 optimal weight: 0.9990 chunk 296 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN b 235 ASN b 545 HIS b 622 HIS d 621 GLN e 57 ASN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.174385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131659 restraints weight = 53817.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129271 restraints weight = 58934.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130883 restraints weight = 65938.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131027 restraints weight = 39091.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132047 restraints weight = 35937.813| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 41520 Z= 0.244 Angle : 0.651 10.827 56472 Z= 0.340 Chirality : 0.045 0.198 6144 Planarity : 0.005 0.061 7332 Dihedral : 4.630 28.491 5700 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.29 % Allowed : 10.70 % Favored : 86.01 % 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 aren not related in a simple way. whole: 1.11 (0.12), residues: 5004 helix: 2.10 (0.10), residues: 2820 sheet: 0.07 (0.23), residues: 492 loop : -1.49 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 237 TYR 0.034 0.002 TYR i 608 PHE 0.046 0.002 PHE h 188 TRP 0.017 0.002 TRP l 241 HIS 0.016 0.002 HIS h 192 Details of bonding type rmsd covalent geometry : bond 0.00606 (41520) covalent geometry : angle 0.65060 (56472) hydrogen bonds : bond 0.05692 ( 2315) hydrogen bonds : angle 4.25899 ( 6696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 462 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 523 GLN cc_start: 0.7427 (mp10) cc_final: 0.7090 (mp10) REVERT: a 615 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7546 (mt) REVERT: b 608 TYR cc_start: 0.7817 (m-10) cc_final: 0.7356 (m-80) REVERT: c 47 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8778 (pp) REVERT: c 237 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7119 (mmp-170) REVERT: d 592 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8019 (tm-30) REVERT: e 47 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8594 (pp) REVERT: e 615 LEU cc_start: 0.8960 (mm) cc_final: 0.8474 (mm) REVERT: f 160 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8325 (t80) REVERT: f 528 LEU cc_start: 0.8364 (tp) cc_final: 0.8147 (tp) REVERT: g 176 ARG cc_start: 0.7240 (mmm160) cc_final: 0.7016 (mmm-85) REVERT: g 219 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: h 127 TRP cc_start: 0.8246 (t60) cc_final: 0.7870 (t60) REVERT: h 219 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.6998 (m-80) REVERT: h 592 GLU cc_start: 0.7858 (tp30) cc_final: 0.7549 (tt0) REVERT: j 541 LYS cc_start: 0.7949 (mttt) cc_final: 0.7670 (mttm) REVERT: k 136 LEU cc_start: 0.8069 (tp) cc_final: 0.7451 (tp) REVERT: k 219 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: l 47 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8480 (pt) REVERT: l 557 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7566 (m-10) outliers start: 139 outliers final: 102 residues processed: 558 average time/residue: 0.2395 time to fit residues: 216.5314 Evaluate side-chains 543 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 432 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 160 TYR Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 155 SER Chi-restraints excluded: chain b residue 191 GLN Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 496 ILE Chi-restraints excluded: chain b residue 537 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 586 SER Chi-restraints excluded: chain c residue 589 ILE Chi-restraints excluded: chain c residue 607 THR Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 57 ASN Chi-restraints excluded: chain e residue 75 HIS Chi-restraints excluded: chain e residue 131 LEU Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 497 ILE Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain e residue 584 THR Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 160 TYR Chi-restraints excluded: chain f residue 219 PHE Chi-restraints excluded: chain f residue 222 THR Chi-restraints excluded: chain f residue 253 GLU Chi-restraints excluded: chain f residue 255 LEU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain f residue 572 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 166 CYS Chi-restraints excluded: chain g residue 219 PHE Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 255 LEU Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 590 LEU Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 142 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 219 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain h residue 494 TYR Chi-restraints excluded: chain h residue 588 VAL Chi-restraints excluded: chain h residue 589 ILE Chi-restraints excluded: chain i residue 43 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 219 PHE Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 256 VAL Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 178 GLU Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 295 LEU Chi-restraints excluded: chain k residue 304 LEU Chi-restraints excluded: chain k residue 497 ILE Chi-restraints excluded: chain l residue 43 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 161 ILE Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 257 LEU Chi-restraints excluded: chain l residue 292 VAL Chi-restraints excluded: chain l residue 310 ASP Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 557 TYR Chi-restraints excluded: chain l residue 558 SER Chi-restraints excluded: chain l residue 589 ILE Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 419 optimal weight: 0.4980 chunk 228 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 486 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 191 GLN b 57 ASN b 235 ASN ** c 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 606 GLN d 621 GLN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 606 GLN ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.178312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137146 restraints weight = 53548.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134056 restraints weight = 79643.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135792 restraints weight = 72346.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136002 restraints weight = 47506.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137245 restraints weight = 42345.215| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41520 Z= 0.128 Angle : 0.547 12.067 56472 Z= 0.285 Chirality : 0.040 0.201 6144 Planarity : 0.004 0.050 7332 Dihedral : 4.269 27.789 5700 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 12.45 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.12), residues: 5004 helix: 2.41 (0.10), residues: 2820 sheet: 0.07 (0.23), residues: 504 loop : -1.35 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG d 251 TYR 0.033 0.001 TYR a 608 PHE 0.033 0.001 PHE h 188 TRP 0.018 0.001 TRP b 127 HIS 0.008 0.001 HIS l 93 Details of bonding type rmsd covalent geometry : bond 0.00290 (41520) covalent geometry : angle 0.54659 (56472) hydrogen bonds : bond 0.04463 ( 2315) hydrogen bonds : angle 4.01172 ( 6696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 476 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 523 GLN cc_start: 0.7432 (mp10) cc_final: 0.7115 (mp10) REVERT: a 615 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7348 (mt) REVERT: b 608 TYR cc_start: 0.7763 (m-10) cc_final: 0.7274 (m-80) REVERT: c 47 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8650 (pp) REVERT: c 237 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7162 (mmp-170) REVERT: c 304 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8260 (tt) REVERT: d 545 HIS cc_start: 0.8154 (m90) cc_final: 0.7862 (m90) REVERT: d 589 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8836 (pt) REVERT: d 592 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7794 (tm-30) REVERT: e 47 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8513 (pp) REVERT: e 497 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8519 (tt) REVERT: e 615 LEU cc_start: 0.8932 (mm) cc_final: 0.8450 (mm) REVERT: g 219 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: g 612 ILE cc_start: 0.8715 (mt) cc_final: 0.8441 (tp) REVERT: h 47 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7957 (pp) REVERT: h 127 TRP cc_start: 0.8228 (t60) cc_final: 0.7864 (t60) REVERT: h 592 GLU cc_start: 0.7676 (tp30) cc_final: 0.7164 (tt0) REVERT: i 136 LEU cc_start: 0.7933 (tt) cc_final: 0.7720 (tt) REVERT: j 541 LYS cc_start: 0.7865 (mttt) cc_final: 0.7488 (mttm) REVERT: k 47 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8607 (pp) REVERT: k 136 LEU cc_start: 0.7924 (tp) cc_final: 0.7165 (tp) REVERT: k 219 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: l 47 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8303 (pp) outliers start: 109 outliers final: 64 residues processed: 551 average time/residue: 0.2189 time to fit residues: 194.8125 Evaluate side-chains 512 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 437 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 192 HIS Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 503 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 219 PHE Chi-restraints excluded: chain c residue 304 LEU Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 586 SER Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 497 ILE Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain e residue 606 GLN Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 503 MET Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain f residue 572 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 166 CYS Chi-restraints excluded: chain g residue 219 PHE Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 231 TYR Chi-restraints excluded: chain h residue 497 ILE Chi-restraints excluded: chain h residue 589 ILE Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 219 PHE Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 256 VAL Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 222 THR Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 295 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 267 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 384 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 471 optimal weight: 8.9990 chunk 413 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 191 GLN b 57 ASN b 235 ASN d 606 GLN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 549 GLN ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132234 restraints weight = 53876.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129380 restraints weight = 59506.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131273 restraints weight = 63418.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131257 restraints weight = 41086.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131931 restraints weight = 38891.394| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 41520 Z= 0.228 Angle : 0.637 11.500 56472 Z= 0.330 Chirality : 0.043 0.230 6144 Planarity : 0.005 0.067 7332 Dihedral : 4.455 28.688 5700 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.12 % Allowed : 12.59 % Favored : 84.28 % 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 aren not related in a simple way. whole: 1.14 (0.12), residues: 5004 helix: 2.14 (0.10), residues: 2820 sheet: -0.09 (0.23), residues: 504 loop : -1.46 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG d 251 TYR 0.037 0.002 TYR a 608 PHE 0.029 0.002 PHE h 188 TRP 0.040 0.002 TRP b 127 HIS 0.012 0.001 HIS g 31 Details of bonding type rmsd covalent geometry : bond 0.00568 (41520) covalent geometry : angle 0.63722 (56472) hydrogen bonds : bond 0.05370 ( 2315) hydrogen bonds : angle 4.18536 ( 6696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 437 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 543 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7231 (tt) REVERT: a 615 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7604 (mt) REVERT: b 608 TYR cc_start: 0.7819 (m-10) cc_final: 0.7324 (m-80) REVERT: c 47 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8773 (pp) REVERT: c 124 PHE cc_start: 0.8349 (t80) cc_final: 0.7929 (t80) REVERT: c 237 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7080 (mmp-170) REVERT: c 304 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (tt) REVERT: d 251 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6904 (mmm-85) REVERT: d 545 HIS cc_start: 0.8233 (m90) cc_final: 0.7889 (m90) REVERT: d 589 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8736 (pt) REVERT: d 592 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7917 (tm-30) REVERT: e 47 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8588 (pp) REVERT: e 615 LEU cc_start: 0.8967 (mm) cc_final: 0.8468 (mm) REVERT: f 160 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8372 (t80) REVERT: f 528 LEU cc_start: 0.8397 (tp) cc_final: 0.8168 (tp) REVERT: g 219 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: h 127 TRP cc_start: 0.8243 (t60) cc_final: 0.7853 (t60) REVERT: h 219 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: h 592 GLU cc_start: 0.7715 (tp30) cc_final: 0.7176 (tt0) REVERT: i 43 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8560 (mp) REVERT: j 128 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.8329 (ptm160) REVERT: j 541 LYS cc_start: 0.7891 (mttt) cc_final: 0.7596 (mttm) REVERT: k 136 LEU cc_start: 0.7925 (tp) cc_final: 0.7317 (tp) REVERT: k 156 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8123 (p) REVERT: k 219 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: l 43 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8750 (mp) REVERT: l 47 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8438 (pt) REVERT: l 125 ASP cc_start: 0.8070 (t70) cc_final: 0.7671 (t0) outliers start: 132 outliers final: 103 residues processed: 534 average time/residue: 0.2113 time to fit residues: 184.0587 Evaluate side-chains 543 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 426 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 160 TYR Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 292 VAL Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 543 LEU Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 155 SER Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 292 VAL Chi-restraints excluded: chain b residue 496 ILE Chi-restraints excluded: chain b residue 503 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 219 PHE Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 304 LEU Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 586 SER Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain d residue 589 ILE Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 131 LEU Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain e residue 574 LEU Chi-restraints excluded: chain e residue 584 THR Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 160 TYR Chi-restraints excluded: chain f residue 219 PHE Chi-restraints excluded: chain f residue 253 GLU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 292 VAL Chi-restraints excluded: chain f residue 503 MET Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain f residue 572 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 166 CYS Chi-restraints excluded: chain g residue 219 PHE Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain g residue 590 LEU Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 142 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 219 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain h residue 497 ILE Chi-restraints excluded: chain h residue 588 VAL Chi-restraints excluded: chain h residue 589 ILE Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 43 LEU Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 219 PHE Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 230 VAL Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain i residue 590 LEU Chi-restraints excluded: chain j residue 47 LEU Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 256 VAL Chi-restraints excluded: chain j residue 594 GLU Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 75 HIS Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 156 SER Chi-restraints excluded: chain k residue 178 GLU Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 222 THR Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 295 LEU Chi-restraints excluded: chain l residue 43 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 161 ILE Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 257 LEU Chi-restraints excluded: chain l residue 292 VAL Chi-restraints excluded: chain l residue 310 ASP Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 558 SER Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 146 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 417 optimal weight: 6.9990 chunk 483 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 545 HIS b 57 ASN ** c 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 621 GLN e 57 ASN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 606 GLN ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137159 restraints weight = 53272.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134069 restraints weight = 80118.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135965 restraints weight = 71644.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136150 restraints weight = 47130.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136847 restraints weight = 41298.821| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41520 Z= 0.123 Angle : 0.550 10.325 56472 Z= 0.285 Chirality : 0.040 0.223 6144 Planarity : 0.004 0.047 7332 Dihedral : 4.146 28.768 5700 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 13.80 % Favored : 83.85 % 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 aren not related in a simple way. whole: 1.47 (0.12), residues: 5004 helix: 2.42 (0.10), residues: 2820 sheet: 0.12 (0.23), residues: 504 loop : -1.37 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 237 TYR 0.042 0.001 TYR a 608 PHE 0.028 0.001 PHE h 188 TRP 0.046 0.001 TRP b 127 HIS 0.009 0.001 HIS l 93 Details of bonding type rmsd covalent geometry : bond 0.00279 (41520) covalent geometry : angle 0.55005 (56472) hydrogen bonds : bond 0.04211 ( 2315) hydrogen bonds : angle 3.97272 ( 6696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 461 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 132 ARG cc_start: 0.8249 (ttp80) cc_final: 0.8044 (tmm-80) REVERT: a 244 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6886 (ptm-80) REVERT: a 615 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7548 (mt) REVERT: b 608 TYR cc_start: 0.7745 (m-10) cc_final: 0.7170 (m-80) REVERT: c 47 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8635 (pp) REVERT: c 124 PHE cc_start: 0.8233 (t80) cc_final: 0.7826 (t80) REVERT: c 237 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7099 (mmp-170) REVERT: c 304 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8305 (tt) REVERT: d 503 MET cc_start: 0.7538 (tmm) cc_final: 0.7209 (tmm) REVERT: d 545 HIS cc_start: 0.8152 (m90) cc_final: 0.7864 (m90) REVERT: d 557 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8391 (m-10) REVERT: d 592 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7728 (tm-30) REVERT: e 615 LEU cc_start: 0.8999 (mm) cc_final: 0.8491 (mm) REVERT: g 219 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: h 47 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7883 (pp) REVERT: h 69 LEU cc_start: 0.8253 (tp) cc_final: 0.7934 (tt) REVERT: h 127 TRP cc_start: 0.8212 (t60) cc_final: 0.7809 (t60) REVERT: h 196 ARG cc_start: 0.7581 (ptt-90) cc_final: 0.7225 (ptt-90) REVERT: h 219 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: h 501 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8144 (ptpt) REVERT: h 592 GLU cc_start: 0.7492 (tp30) cc_final: 0.7145 (tt0) REVERT: j 541 LYS cc_start: 0.7776 (mttt) cc_final: 0.7391 (mttm) REVERT: k 47 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (pp) REVERT: k 136 LEU cc_start: 0.7883 (tp) cc_final: 0.7213 (tp) REVERT: k 156 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8017 (p) REVERT: k 219 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: l 47 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8194 (pp) REVERT: l 128 ARG cc_start: 0.8322 (ttt180) cc_final: 0.8086 (ttp-110) outliers start: 99 outliers final: 72 residues processed: 531 average time/residue: 0.2126 time to fit residues: 181.5915 Evaluate side-chains 521 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 437 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 160 TYR Chi-restraints excluded: chain a residue 192 HIS Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 244 ARG Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain a residue 615 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 155 SER Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 496 ILE Chi-restraints excluded: chain b residue 503 MET Chi-restraints excluded: chain b residue 537 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 219 PHE Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 304 LEU Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 586 SER Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 557 TYR Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain e residue 57 ASN Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 253 GLU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 166 CYS Chi-restraints excluded: chain g residue 219 PHE Chi-restraints excluded: chain g residue 222 THR Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 142 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 219 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain h residue 292 VAL Chi-restraints excluded: chain h residue 589 ILE Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 219 PHE Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 230 VAL Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 29 LYS Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 256 VAL Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 142 LEU Chi-restraints excluded: chain k residue 156 SER Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 295 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 556 SER Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 364 optimal weight: 0.0170 chunk 168 optimal weight: 0.3980 chunk 176 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 466 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 413 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN ** c 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 621 GLN e 192 HIS ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.181780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137463 restraints weight = 53303.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134389 restraints weight = 60500.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136455 restraints weight = 58116.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136831 restraints weight = 38843.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137370 restraints weight = 33232.808| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 41520 Z= 0.109 Angle : 0.533 12.388 56472 Z= 0.274 Chirality : 0.039 0.274 6144 Planarity : 0.004 0.043 7332 Dihedral : 3.933 27.538 5700 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.92 % Allowed : 14.25 % Favored : 83.83 % 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 aren not related in a simple way. whole: 1.68 (0.12), residues: 5004 helix: 2.56 (0.10), residues: 2820 sheet: 0.39 (0.24), residues: 504 loop : -1.27 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG c 84 TYR 0.031 0.001 TYR a 608 PHE 0.026 0.001 PHE h 188 TRP 0.054 0.001 TRP b 127 HIS 0.010 0.001 HIS l 93 Details of bonding type rmsd covalent geometry : bond 0.00229 (41520) covalent geometry : angle 0.53278 (56472) hydrogen bonds : bond 0.03759 ( 2315) hydrogen bonds : angle 3.84400 ( 6696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 462 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 132 ARG cc_start: 0.8238 (ttp80) cc_final: 0.8016 (tmm-80) REVERT: b 608 TYR cc_start: 0.7755 (m-10) cc_final: 0.7395 (m-80) REVERT: c 47 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8488 (pp) REVERT: c 124 PHE cc_start: 0.8261 (t80) cc_final: 0.7890 (t80) REVERT: c 237 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7086 (mmp-170) REVERT: c 304 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8275 (tt) REVERT: c 545 HIS cc_start: 0.7768 (m90) cc_final: 0.7295 (m90) REVERT: d 128 ARG cc_start: 0.7491 (ptm160) cc_final: 0.7233 (ptm160) REVERT: d 503 MET cc_start: 0.7645 (tmm) cc_final: 0.7338 (tmm) REVERT: d 545 HIS cc_start: 0.8163 (m90) cc_final: 0.7834 (m90) REVERT: d 557 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: d 592 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7761 (tm-30) REVERT: e 57 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8285 (m110) REVERT: e 606 GLN cc_start: 0.7789 (tp40) cc_final: 0.7554 (tp40) REVERT: e 615 LEU cc_start: 0.8993 (mm) cc_final: 0.8470 (mm) REVERT: f 33 THR cc_start: 0.8683 (t) cc_final: 0.8348 (t) REVERT: g 47 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8162 (pp) REVERT: g 219 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: h 47 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7728 (pp) REVERT: h 69 LEU cc_start: 0.8169 (tp) cc_final: 0.7870 (tt) REVERT: h 127 TRP cc_start: 0.8173 (t60) cc_final: 0.7802 (t60) REVERT: h 196 ARG cc_start: 0.7565 (ptt-90) cc_final: 0.7223 (ptt-90) REVERT: h 219 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: h 592 GLU cc_start: 0.7478 (tp30) cc_final: 0.7166 (tt0) REVERT: j 541 LYS cc_start: 0.7640 (mttt) cc_final: 0.7233 (mttm) REVERT: j 549 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6819 (pm20) REVERT: k 47 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8291 (pp) REVERT: k 136 LEU cc_start: 0.7875 (tp) cc_final: 0.7188 (tp) REVERT: k 156 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.7938 (p) REVERT: k 219 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: l 47 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8095 (pp) REVERT: l 288 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7661 (tp30) REVERT: l 592 GLU cc_start: 0.7508 (tp30) cc_final: 0.7095 (tm-30) outliers start: 81 outliers final: 54 residues processed: 521 average time/residue: 0.2087 time to fit residues: 175.3862 Evaluate side-chains 505 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 439 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 503 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 219 PHE Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 304 LEU Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 586 SER Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 557 TYR Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain e residue 57 ASN Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 192 HIS Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 162 ASP Chi-restraints excluded: chain g residue 219 PHE Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 219 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 156 SER Chi-restraints excluded: chain k residue 178 GLU Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 222 THR Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 295 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 356 optimal weight: 0.7980 chunk 322 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 444 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 326 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 235 ASN ** c 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 606 GLN ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 140 HIS ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135085 restraints weight = 53357.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131117 restraints weight = 70811.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133206 restraints weight = 61698.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133922 restraints weight = 39167.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134253 restraints weight = 36321.519| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41520 Z= 0.159 Angle : 0.577 11.602 56472 Z= 0.296 Chirality : 0.041 0.267 6144 Planarity : 0.005 0.069 7332 Dihedral : 4.038 27.547 5700 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.06 % Allowed : 14.23 % Favored : 83.71 % 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 aren not related in a simple way. whole: 1.53 (0.12), residues: 5004 helix: 2.45 (0.10), residues: 2820 sheet: 0.25 (0.24), residues: 504 loop : -1.34 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG i 251 TYR 0.030 0.001 TYR c 608 PHE 0.024 0.001 PHE h 188 TRP 0.062 0.001 TRP b 127 HIS 0.009 0.001 HIS l 93 Details of bonding type rmsd covalent geometry : bond 0.00387 (41520) covalent geometry : angle 0.57704 (56472) hydrogen bonds : bond 0.04387 ( 2315) hydrogen bonds : angle 3.93765 ( 6696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 441 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 132 ARG cc_start: 0.8268 (ttp80) cc_final: 0.8065 (tmm-80) REVERT: c 47 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8634 (pp) REVERT: c 124 PHE cc_start: 0.8256 (t80) cc_final: 0.7883 (t80) REVERT: c 237 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7090 (mmp-170) REVERT: c 304 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8338 (tt) REVERT: c 545 HIS cc_start: 0.7996 (m90) cc_final: 0.7580 (m90) REVERT: d 128 ARG cc_start: 0.7470 (ptm160) cc_final: 0.7243 (ptm160) REVERT: d 503 MET cc_start: 0.7653 (tmm) cc_final: 0.7359 (tmm) REVERT: d 545 HIS cc_start: 0.8278 (m90) cc_final: 0.7984 (m90) REVERT: d 557 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8344 (m-10) REVERT: d 592 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7861 (tm-30) REVERT: e 615 LEU cc_start: 0.9031 (mm) cc_final: 0.8499 (mm) REVERT: g 47 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8241 (pp) REVERT: g 219 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: h 47 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7929 (pp) REVERT: h 127 TRP cc_start: 0.8194 (t60) cc_final: 0.7763 (t60) REVERT: h 196 ARG cc_start: 0.7465 (ptt-90) cc_final: 0.7153 (ptt-90) REVERT: h 219 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: h 592 GLU cc_start: 0.7539 (tp30) cc_final: 0.7332 (tt0) REVERT: j 128 ARG cc_start: 0.8677 (ptp-170) cc_final: 0.8460 (ptm160) REVERT: j 541 LYS cc_start: 0.7801 (mttt) cc_final: 0.7460 (mttm) REVERT: j 549 GLN cc_start: 0.7068 (tm-30) cc_final: 0.6844 (pm20) REVERT: k 47 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8391 (pp) REVERT: k 136 LEU cc_start: 0.7778 (tp) cc_final: 0.7159 (tp) REVERT: k 156 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.7981 (p) REVERT: k 219 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: l 47 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8212 (pp) REVERT: l 557 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7846 (m-10) REVERT: l 592 GLU cc_start: 0.7536 (tp30) cc_final: 0.7112 (tm-30) outliers start: 87 outliers final: 68 residues processed: 505 average time/residue: 0.2146 time to fit residues: 174.5679 Evaluate side-chains 512 residues out of total 4224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 432 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 75 HIS Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain a residue 160 TYR Chi-restraints excluded: chain a residue 192 HIS Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 496 ILE Chi-restraints excluded: chain a residue 503 MET Chi-restraints excluded: chain a residue 544 CYS Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 75 HIS Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 256 VAL Chi-restraints excluded: chain b residue 503 MET Chi-restraints excluded: chain b residue 537 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 219 PHE Chi-restraints excluded: chain c residue 256 VAL Chi-restraints excluded: chain c residue 304 LEU Chi-restraints excluded: chain c residue 494 TYR Chi-restraints excluded: chain c residue 586 SER Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain d residue 557 TYR Chi-restraints excluded: chain d residue 586 SER Chi-restraints excluded: chain e residue 57 ASN Chi-restraints excluded: chain e residue 182 THR Chi-restraints excluded: chain e residue 219 PHE Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 542 ILE Chi-restraints excluded: chain e residue 556 SER Chi-restraints excluded: chain e residue 584 THR Chi-restraints excluded: chain f residue 142 LEU Chi-restraints excluded: chain f residue 143 VAL Chi-restraints excluded: chain f residue 253 GLU Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 558 SER Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 75 HIS Chi-restraints excluded: chain g residue 162 ASP Chi-restraints excluded: chain g residue 166 CYS Chi-restraints excluded: chain g residue 219 PHE Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain g residue 256 VAL Chi-restraints excluded: chain g residue 292 VAL Chi-restraints excluded: chain h residue 47 LEU Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 219 PHE Chi-restraints excluded: chain h residue 256 VAL Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 222 THR Chi-restraints excluded: chain i residue 230 VAL Chi-restraints excluded: chain i residue 256 VAL Chi-restraints excluded: chain i residue 496 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 86 LEU Chi-restraints excluded: chain j residue 222 THR Chi-restraints excluded: chain j residue 230 VAL Chi-restraints excluded: chain j residue 256 VAL Chi-restraints excluded: chain k residue 47 LEU Chi-restraints excluded: chain k residue 128 ARG Chi-restraints excluded: chain k residue 156 SER Chi-restraints excluded: chain k residue 178 GLU Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 222 THR Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 256 VAL Chi-restraints excluded: chain k residue 295 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 248 SER Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 256 VAL Chi-restraints excluded: chain l residue 557 TYR Chi-restraints excluded: chain l residue 612 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 304 optimal weight: 0.0970 chunk 394 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 471 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 392 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 431 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 235 ASN ** c 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 606 GLN ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136236 restraints weight = 53459.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132471 restraints weight = 69503.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135340 restraints weight = 59251.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135349 restraints weight = 37805.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136050 restraints weight = 34748.857| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41520 Z= 0.126 Angle : 0.556 11.345 56472 Z= 0.285 Chirality : 0.040 0.234 6144 Planarity : 0.004 0.058 7332 Dihedral : 3.967 27.338 5700 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.06 % Allowed : 14.28 % Favored : 83.66 % 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 aren not related in a simple way. whole: 1.58 (0.12), residues: 5004 helix: 2.49 (0.10), residues: 2820 sheet: 0.31 (0.24), residues: 504 loop : -1.32 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG i 251 TYR 0.037 0.001 TYR l 608 PHE 0.024 0.001 PHE h 188 TRP 0.062 0.001 TRP b 127 HIS 0.009 0.001 HIS l 93 Details of bonding type rmsd covalent geometry : bond 0.00293 (41520) covalent geometry : angle 0.55584 (56472) hydrogen bonds : bond 0.04066 ( 2315) hydrogen bonds : angle 3.88114 ( 6696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5727.31 seconds wall clock time: 99 minutes 47.38 seconds (5987.38 seconds total)