Starting phenix.real_space_refine on Tue Aug 26 17:57:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opc_70691/08_2025/9opc_70691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opc_70691/08_2025/9opc_70691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9opc_70691/08_2025/9opc_70691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opc_70691/08_2025/9opc_70691.map" model { file = "/net/cci-nas-00/data/ceres_data/9opc_70691/08_2025/9opc_70691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opc_70691/08_2025/9opc_70691.cif" } resolution = 4.2 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 25236 2.51 5 N 7188 2.21 5 O 7104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 39636 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "b" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "c" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "d" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "e" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "f" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "g" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "h" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "i" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "j" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "k" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "l" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3303 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Time building chain proxies: 6.97, per 1000 atoms: 0.18 Number of scatterers: 39636 At special positions: 0 Unit cell: (158.4, 159.5, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 7104 8.00 N 7188 7.00 C 25236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 60 sheets defined 63.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'a' and resid 33 through 44 removed outlier: 3.792A 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: 3.758A pdb=" N VAL a 59 " --> pdb=" O VAL a 55 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG a 60 " --> pdb=" O TYR a 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 55 through 60' Processing helix chain 'a' and resid 62 through 79 Processing helix chain 'a' and resid 82 through 98 Processing helix chain 'a' and resid 100 through 109 Processing helix chain 'a' and resid 112 through 147 Processing helix chain 'a' and resid 156 through 167 Processing helix chain 'a' and resid 179 through 190 removed outlier: 4.003A pdb=" N LYS a 190 " --> pdb=" O ARG a 186 " (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: 3.800A pdb=" N ALA a 282 " --> pdb=" O PRO a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 540 removed outlier: 4.083A pdb=" N PHE a 540 " --> pdb=" O LEU a 536 " (cutoff:3.500A) Processing helix chain 'a' and resid 558 through 572 removed outlier: 4.633A 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 584 through 590 removed outlier: 4.025A pdb=" N VAL a 588 " --> pdb=" O THR a 584 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE a 589 " --> pdb=" O GLY a 585 " (cutoff:3.500A) Processing helix chain 'a' and resid 591 through 603 removed outlier: 3.856A pdb=" N LEU a 595 " --> pdb=" O GLY a 591 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR a 603 " --> pdb=" O VAL a 599 " (cutoff:3.500A) Processing helix chain 'a' and resid 603 through 623 removed outlier: 3.733A pdb=" N THR a 607 " --> pdb=" O THR a 603 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 44 removed outlier: 3.818A pdb=" N MET b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 54 Processing helix chain 'b' and resid 55 through 60 removed outlier: 3.709A pdb=" N VAL b 59 " --> pdb=" O VAL b 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG b 60 " --> pdb=" O TYR b 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 55 through 60' Processing helix chain 'b' and resid 62 through 79 Processing helix chain 'b' and resid 82 through 98 Processing helix chain 'b' and resid 100 through 109 Processing helix chain 'b' and resid 112 through 147 removed outlier: 3.767A pdb=" N ILE b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 156 through 167 Processing helix chain 'b' and resid 179 through 191 removed outlier: 3.543A pdb=" N GLN b 191 " --> pdb=" O ALA b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.157A pdb=" N THR b 195 " --> 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: 3.563A pdb=" N ASN b 297 " --> pdb=" O CYS b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 521 through 540 removed outlier: 3.820A pdb=" N PHE b 540 " --> pdb=" O LEU b 536 " (cutoff:3.500A) Processing helix chain 'b' and resid 558 through 573 removed outlier: 4.572A 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 590 removed outlier: 4.217A pdb=" N VAL b 588 " --> pdb=" O THR b 584 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE b 589 " --> pdb=" O GLY b 585 " (cutoff:3.500A) Processing helix chain 'b' and resid 591 through 603 removed outlier: 3.712A pdb=" N LYS b 602 " --> pdb=" O ALA b 598 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR b 603 " --> pdb=" O VAL b 599 " (cutoff:3.500A) Processing helix chain 'b' and resid 603 through 623 removed outlier: 3.882A pdb=" N THR b 607 " --> pdb=" O THR b 603 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 44 removed outlier: 3.894A 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: 3.732A pdb=" N VAL c 59 " --> pdb=" O VAL c 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG c 60 " --> pdb=" O TYR c 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 55 through 60' Processing helix chain 'c' and resid 62 through 79 Processing helix chain 'c' and resid 82 through 98 Processing helix chain 'c' and resid 100 through 109 Processing helix chain 'c' and resid 112 through 147 removed outlier: 3.808A pdb=" N ILE c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 156 through 167 Processing helix chain 'c' and resid 179 through 190 removed outlier: 3.966A pdb=" N LYS c 190 " --> pdb=" O ARG c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 193 through 198 removed outlier: 3.658A pdb=" N GLN c 197 " --> pdb=" O PRO c 193 " (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 Processing helix chain 'c' and resid 501 through 503 No H-bonds generated for 'chain 'c' and resid 501 through 503' Processing helix chain 'c' and resid 521 through 540 removed outlier: 3.691A pdb=" N PHE c 540 " --> pdb=" O LEU c 536 " (cutoff:3.500A) Processing helix chain 'c' and resid 558 through 573 removed outlier: 4.847A 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: 3.795A pdb=" N LYS c 602 " --> pdb=" O ALA c 598 " (cutoff:3.500A) Processing helix chain 'c' and resid 603 through 623 removed outlier: 3.543A pdb=" N THR c 607 " --> pdb=" O THR c 603 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 44 removed outlier: 3.764A pdb=" N MET d 37 " --> pdb=" O THR d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 54 Processing helix chain 'd' and resid 55 through 60 removed outlier: 3.751A pdb=" N VAL d 59 " --> pdb=" O VAL d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 79 Processing helix chain 'd' and resid 82 through 98 Processing helix chain 'd' and resid 100 through 109 Processing helix chain 'd' and resid 112 through 147 Processing helix chain 'd' and resid 156 through 167 Processing helix chain 'd' and resid 179 through 190 removed outlier: 3.978A pdb=" N LYS d 190 " --> pdb=" O ARG d 186 " (cutoff:3.500A) Processing helix chain 'd' and resid 193 through 198 Processing helix chain 'd' and resid 198 through 221 removed outlier: 3.605A pdb=" N ALA d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 226 through 230 removed outlier: 4.145A pdb=" N VAL d 230 " --> pdb=" O TYR d 227 " (cutoff:3.500A) Processing helix chain 'd' and resid 271 through 297 Proline residue: d 278 - end of helix Processing helix chain 'd' and resid 501 through 504 Processing helix chain 'd' and resid 521 through 540 removed outlier: 3.740A pdb=" N PHE d 540 " --> pdb=" O LEU d 536 " (cutoff:3.500A) Processing helix chain 'd' and resid 558 through 573 removed outlier: 4.665A 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: 3.852A pdb=" N VAL d 588 " --> pdb=" O THR d 584 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE d 589 " --> pdb=" O GLY d 585 " (cutoff:3.500A) Processing helix chain 'd' and resid 591 through 603 removed outlier: 3.646A pdb=" N LYS d 602 " --> pdb=" O ALA d 598 " (cutoff:3.500A) Processing helix chain 'd' and resid 603 through 623 removed outlier: 4.080A pdb=" N THR d 607 " --> pdb=" O THR d 603 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU d 615 " --> pdb=" O ASP d 611 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL d 620 " --> pdb=" O PHE d 616 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN d 621 " --> pdb=" O VAL d 617 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 44 removed outlier: 3.950A pdb=" N MET e 37 " --> pdb=" O THR e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 54 Processing helix chain 'e' and resid 55 through 61 Processing helix chain 'e' and resid 62 through 79 removed outlier: 3.954A pdb=" N THR e 66 " --> pdb=" O SER e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 98 Processing helix chain 'e' and resid 100 through 109 Processing helix chain 'e' and resid 112 through 147 Processing helix chain 'e' and resid 148 through 150 No H-bonds generated for 'chain 'e' and resid 148 through 150' Processing helix chain 'e' and resid 156 through 167 Processing helix chain 'e' and resid 179 through 191 removed outlier: 4.537A pdb=" N GLN e 191 " --> pdb=" O ALA e 187 " (cutoff:3.500A) Processing helix chain 'e' and resid 193 through 198 removed outlier: 3.604A pdb=" N GLN e 197 " --> pdb=" O PRO e 193 " (cutoff:3.500A) 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 Processing helix chain 'e' and resid 521 through 541 removed outlier: 3.819A pdb=" N PHE e 540 " --> pdb=" O LEU e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 558 through 573 removed outlier: 4.574A 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 584 through 590 removed outlier: 3.923A pdb=" N VAL e 588 " --> pdb=" O THR e 584 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE e 589 " --> pdb=" O GLY e 585 " (cutoff:3.500A) Processing helix chain 'e' and resid 591 through 602 removed outlier: 3.503A pdb=" N LEU e 595 " --> pdb=" O GLY e 591 " (cutoff:3.500A) Processing helix chain 'e' and resid 603 through 623 Processing helix chain 'f' and resid 33 through 44 removed outlier: 3.818A pdb=" N MET f 37 " --> pdb=" O THR f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 54 Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.566A pdb=" N VAL f 59 " --> pdb=" O VAL f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 62 through 79 Processing helix chain 'f' and resid 82 through 98 Processing helix chain 'f' and resid 100 through 109 Processing helix chain 'f' and resid 112 through 147 Processing helix chain 'f' and resid 156 through 167 Processing helix chain 'f' and resid 179 through 190 removed outlier: 3.944A pdb=" N LYS f 190 " --> pdb=" O ARG f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 198 removed outlier: 3.896A pdb=" N GLN f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU f 198 " --> pdb=" O LEU f 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 193 through 198' 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: 3.542A pdb=" N ASN f 297 " --> pdb=" O CYS f 293 " (cutoff:3.500A) Processing helix chain 'f' and resid 501 through 503 No H-bonds generated for 'chain 'f' and resid 501 through 503' Processing helix chain 'f' and resid 521 through 540 removed outlier: 3.533A pdb=" N PHE f 540 " --> pdb=" O LEU f 536 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 573 removed outlier: 4.400A 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 590 removed outlier: 4.227A pdb=" N ILE f 589 " --> pdb=" O GLY f 585 " (cutoff:3.500A) Processing helix chain 'f' and resid 591 through 603 removed outlier: 3.567A pdb=" N LYS f 602 " --> pdb=" O ALA f 598 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR f 603 " --> pdb=" O VAL f 599 " (cutoff:3.500A) Processing helix chain 'f' and resid 603 through 623 removed outlier: 3.720A pdb=" N THR f 607 " --> pdb=" O THR f 603 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 45 removed outlier: 3.902A pdb=" N MET g 37 " --> pdb=" O THR g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 54 Processing helix chain 'g' and resid 55 through 60 Processing helix chain 'g' and resid 62 through 79 Processing helix chain 'g' and resid 82 through 98 Processing helix chain 'g' and resid 100 through 109 Processing helix chain 'g' and resid 112 through 147 removed outlier: 3.758A pdb=" N ILE g 116 " --> pdb=" O ARG g 112 " (cutoff:3.500A) Processing helix chain 'g' and resid 156 through 167 Processing helix chain 'g' and resid 179 through 192 removed outlier: 3.803A pdb=" N LYS g 190 " --> pdb=" O ARG g 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN g 191 " --> pdb=" O ALA g 187 " (cutoff:3.500A) Processing helix chain 'g' and resid 193 through 198 removed outlier: 3.655A pdb=" N GLN g 197 " --> pdb=" O PRO g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 198 through 221 removed outlier: 4.097A pdb=" N ALA g 202 " --> pdb=" O LEU g 198 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARG g 207 " --> pdb=" O GLU g 203 " (cutoff:3.500A) 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: 3.561A pdb=" N ASN g 297 " --> pdb=" O CYS g 293 " (cutoff:3.500A) Processing helix chain 'g' and resid 521 through 541 removed outlier: 3.861A pdb=" N PHE g 540 " --> pdb=" O LEU g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 558 through 573 removed outlier: 4.918A 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 590 removed outlier: 3.962A pdb=" N VAL g 588 " --> pdb=" O THR g 584 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE g 589 " --> pdb=" O GLY g 585 " (cutoff:3.500A) Processing helix chain 'g' and resid 591 through 603 removed outlier: 4.107A pdb=" N LYS g 601 " --> pdb=" O ASP g 597 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS g 602 " --> pdb=" O ALA g 598 " (cutoff:3.500A) Processing helix chain 'g' and resid 603 through 623 removed outlier: 4.211A pdb=" N THR g 607 " --> pdb=" O THR g 603 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR g 608 " --> pdb=" O ARG g 604 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 44 removed outlier: 4.026A 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: 3.537A pdb=" N VAL h 59 " --> pdb=" O VAL h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 79 Processing helix chain 'h' and resid 82 through 98 Processing helix chain 'h' and resid 100 through 109 Processing helix chain 'h' and resid 112 through 147 Processing helix chain 'h' and resid 148 through 150 No H-bonds generated for 'chain 'h' and resid 148 through 150' Processing helix chain 'h' and resid 156 through 167 Processing helix chain 'h' and resid 179 through 191 removed outlier: 4.287A pdb=" N GLN h 191 " --> pdb=" O ALA h 187 " (cutoff:3.500A) Processing helix chain 'h' and resid 193 through 198 removed outlier: 3.783A pdb=" N GLN h 197 " --> pdb=" O PRO h 193 " (cutoff:3.500A) Processing helix chain 'h' and resid 198 through 221 Proline residue: h 210 - end of helix Processing helix chain 'h' and resid 226 through 230 removed outlier: 3.619A pdb=" N ARG h 229 " --> pdb=" O ASP h 226 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL h 230 " --> pdb=" O TYR h 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 226 through 230' Processing helix chain 'h' and resid 271 through 297 Proline residue: h 278 - end of helix removed outlier: 3.584A pdb=" N ARG h 296 " --> pdb=" O VAL h 292 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN h 297 " --> pdb=" O CYS h 293 " (cutoff:3.500A) Processing helix chain 'h' and resid 501 through 503 No H-bonds generated for 'chain 'h' and resid 501 through 503' Processing helix chain 'h' and resid 521 through 541 removed outlier: 4.083A pdb=" N PHE h 540 " --> pdb=" O LEU h 536 " (cutoff:3.500A) Processing helix chain 'h' and resid 558 through 573 removed outlier: 4.799A 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 591 through 603 removed outlier: 3.634A pdb=" N THR h 603 " --> pdb=" O VAL h 599 " (cutoff:3.500A) Processing helix chain 'h' and resid 603 through 623 removed outlier: 3.883A pdb=" N THR h 607 " --> pdb=" O THR h 603 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 44 removed outlier: 3.842A pdb=" N MET i 37 " --> pdb=" O THR i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 54 Processing helix chain 'i' and resid 55 through 60 removed outlier: 3.594A pdb=" N VAL i 59 " --> pdb=" O VAL i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 62 through 79 Processing helix chain 'i' and resid 82 through 98 Processing helix chain 'i' and resid 100 through 109 Processing helix chain 'i' and resid 112 through 147 removed outlier: 3.666A pdb=" N ILE i 116 " --> pdb=" O ARG i 112 " (cutoff:3.500A) Processing helix chain 'i' and resid 148 through 150 No H-bonds generated for 'chain 'i' and resid 148 through 150' Processing helix chain 'i' and resid 156 through 167 Processing helix chain 'i' and resid 179 through 190 removed outlier: 4.087A pdb=" N LYS i 190 " --> pdb=" O ARG i 186 " (cutoff:3.500A) Processing helix chain 'i' and resid 193 through 198 removed outlier: 3.881A pdb=" N GLN i 197 " --> pdb=" O PRO i 193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU i 198 " --> pdb=" O LEU i 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 193 through 198' Processing helix chain 'i' and resid 198 through 221 removed outlier: 3.546A pdb=" N ALA i 202 " --> pdb=" O LEU i 198 " (cutoff:3.500A) 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: 3.562A pdb=" N ASN i 297 " --> pdb=" O CYS i 293 " (cutoff:3.500A) Processing helix chain 'i' and resid 521 through 541 removed outlier: 3.983A pdb=" N PHE i 540 " --> pdb=" O LEU i 536 " (cutoff:3.500A) Processing helix chain 'i' and resid 558 through 572 removed outlier: 4.558A pdb=" N ALA i 567 " --> pdb=" O ALA i 563 " (cutoff:3.500A) Proline residue: i 568 - end of helix Processing helix chain 'i' and resid 584 through 590 removed outlier: 3.919A pdb=" N VAL i 588 " --> pdb=" O THR i 584 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE i 589 " --> pdb=" O GLY i 585 " (cutoff:3.500A) Processing helix chain 'i' and resid 591 through 602 removed outlier: 3.534A pdb=" N LEU i 595 " --> pdb=" O GLY i 591 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS i 602 " --> pdb=" O ALA i 598 " (cutoff:3.500A) Processing helix chain 'i' and resid 603 through 623 removed outlier: 3.617A pdb=" N THR i 607 " --> pdb=" O THR i 603 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 44 removed outlier: 3.968A pdb=" N MET j 37 " --> pdb=" O THR j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 54 Processing helix chain 'j' and resid 55 through 61 removed outlier: 3.504A pdb=" N VAL j 59 " --> pdb=" O VAL j 55 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 79 Processing helix chain 'j' and resid 82 through 98 Processing helix chain 'j' and resid 100 through 109 Processing helix chain 'j' and resid 112 through 147 Processing helix chain 'j' and resid 156 through 167 removed outlier: 3.533A pdb=" N TYR j 160 " --> pdb=" O SER j 156 " (cutoff:3.500A) Processing helix chain 'j' and resid 179 through 192 removed outlier: 3.870A pdb=" N LYS j 190 " --> pdb=" O ARG j 186 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN j 191 " --> pdb=" O ALA j 187 " (cutoff:3.500A) Processing helix chain 'j' and resid 193 through 197 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: 3.790A pdb=" N ARG j 296 " --> pdb=" O VAL j 292 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN j 297 " --> pdb=" O CYS j 293 " (cutoff:3.500A) Processing helix chain 'j' and resid 499 through 503 removed outlier: 4.153A pdb=" N SER j 502 " --> pdb=" O VAL j 499 " (cutoff:3.500A) Processing helix chain 'j' and resid 521 through 541 removed outlier: 3.751A pdb=" N PHE j 540 " --> pdb=" O LEU j 536 " (cutoff:3.500A) Processing helix chain 'j' and resid 558 through 572 removed outlier: 4.514A 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 591 through 603 removed outlier: 3.818A pdb=" N LYS j 601 " --> pdb=" O ASP j 597 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS j 602 " --> pdb=" O ALA j 598 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR j 603 " --> pdb=" O VAL j 599 " (cutoff:3.500A) Processing helix chain 'j' and resid 603 through 623 removed outlier: 3.693A pdb=" N THR j 607 " --> pdb=" O THR j 603 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.813A 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: 3.655A pdb=" N VAL k 59 " --> pdb=" O VAL k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 62 through 79 Processing helix chain 'k' and resid 82 through 98 Processing helix chain 'k' and resid 100 through 109 Processing helix chain 'k' and resid 112 through 147 Processing helix chain 'k' and resid 156 through 167 Processing helix chain 'k' and resid 179 through 192 removed outlier: 3.930A pdb=" N LYS k 190 " --> pdb=" O ARG k 186 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN k 191 " --> pdb=" O ALA k 187 " (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 Processing helix chain 'k' and resid 521 through 540 removed outlier: 4.105A pdb=" N PHE k 540 " --> pdb=" O LEU k 536 " (cutoff:3.500A) Processing helix chain 'k' and resid 558 through 573 removed outlier: 4.844A pdb=" N ALA k 567 " --> pdb=" O ALA k 563 " (cutoff:3.500A) Proline residue: k 568 - end of helix Processing helix chain 'k' and resid 591 through 603 removed outlier: 3.807A pdb=" N THR k 603 " --> pdb=" O VAL k 599 " (cutoff:3.500A) Processing helix chain 'k' and resid 603 through 623 removed outlier: 3.764A pdb=" N THR k 607 " --> pdb=" O THR k 603 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 44 removed outlier: 3.913A 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: 3.648A pdb=" N VAL l 59 " --> pdb=" O VAL l 55 " (cutoff:3.500A) removed outlier: 3.603A 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 79 Processing helix chain 'l' and resid 82 through 98 Processing helix chain 'l' and resid 100 through 109 Processing helix chain 'l' and resid 112 through 147 Processing helix chain 'l' and resid 156 through 167 Processing helix chain 'l' and resid 179 through 190 removed outlier: 4.095A pdb=" N LYS l 190 " --> pdb=" O ARG l 186 " (cutoff:3.500A) Processing helix chain 'l' and resid 192 through 197 removed outlier: 3.600A pdb=" N GLN l 197 " --> pdb=" O LEU l 194 " (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 Processing helix chain 'l' and resid 501 through 503 No H-bonds generated for 'chain 'l' and resid 501 through 503' Processing helix chain 'l' and resid 521 through 541 removed outlier: 3.520A pdb=" N GLU l 533 " --> pdb=" O SER l 529 " (cutoff:3.500A) Processing helix chain 'l' and resid 558 through 573 removed outlier: 4.861A 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: 3.956A pdb=" N VAL l 588 " --> pdb=" O THR l 584 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE l 589 " --> pdb=" O GLY l 585 " (cutoff:3.500A) Processing helix chain 'l' and resid 591 through 603 removed outlier: 3.637A pdb=" N LEU l 595 " --> pdb=" O GLY l 591 " (cutoff:3.500A) Processing helix chain 'l' and resid 603 through 623 removed outlier: 4.416A 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: 3.547A pdb=" N ASP a 240 " --> pdb=" O ASN a 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 222 through 224 removed outlier: 3.670A pdb=" N LEU a 255 " --> pdb=" O VAL a 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'a' and resid 495 through 499 removed outlier: 3.505A pdb=" N ILE a 496 " --> pdb=" O VAL a 301 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS a 302 " --> pdb=" O SER b 512 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER b 512 " --> pdb=" O LYS a 302 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU a 304 " --> pdb=" O ALA b 510 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR b 508 " --> pdb=" O GLY a 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 508 through 514 removed outlier: 7.188A pdb=" N LEU c 304 " --> pdb=" O ALA a 510 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER a 512 " --> pdb=" O LYS c 302 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS c 302 " --> pdb=" O SER a 512 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL c 301 " --> pdb=" O ILE c 496 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASP c 498 " --> pdb=" O VAL c 301 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL c 303 " --> pdb=" O ASP c 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 542 through 544 Processing sheet with id=AA7, first strand: chain 'b' and resid 26 through 29 Processing sheet with id=AA8, first strand: chain 'b' and resid 222 through 224 removed outlier: 3.643A pdb=" N LEU b 255 " --> pdb=" O VAL b 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 261 through 262 Processing sheet with id=AB1, first strand: chain 'b' and resid 495 through 499 removed outlier: 7.004A pdb=" N VAL b 301 " --> pdb=" O ILE b 496 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASP b 498 " --> pdb=" O VAL b 301 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL b 303 " --> pdb=" O ASP b 498 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS b 302 " --> pdb=" O SER l 512 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER l 512 " --> pdb=" O LYS b 302 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU b 304 " --> pdb=" O ALA l 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 543 through 546 removed outlier: 7.350A pdb=" N LEU b 543 " --> pdb=" O ILE b 555 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE b 555 " --> pdb=" O LEU b 543 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS b 545 " --> pdb=" O THR b 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 26 through 29 Processing sheet with id=AB4, first strand: chain 'c' and resid 222 through 224 removed outlier: 3.667A pdb=" N LEU c 255 " --> pdb=" O VAL c 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 261 through 262 Processing sheet with id=AB6, first strand: chain 'c' and resid 508 through 514 removed outlier: 3.574A pdb=" N TYR c 508 " --> pdb=" O GLY d 306 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU d 304 " --> pdb=" O ALA c 510 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER c 512 " --> pdb=" O LYS d 302 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS d 302 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL d 301 " --> pdb=" O ILE d 496 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP d 498 " --> pdb=" O VAL d 301 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL d 303 " --> pdb=" O ASP d 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 543 through 546 removed outlier: 7.043A pdb=" N LEU c 543 " --> pdb=" O ILE c 555 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE c 555 " --> pdb=" O LEU c 543 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N HIS c 545 " --> pdb=" O THR c 553 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 26 through 29 removed outlier: 3.603A pdb=" N TYR d 231 " --> pdb=" O ARG d 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 244 " --> pdb=" O TYR d 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 222 through 224 removed outlier: 3.592A pdb=" N LEU d 255 " --> pdb=" O VAL d 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 261 through 262 Processing sheet with id=AC2, first strand: chain 'd' and resid 508 through 514 removed outlier: 7.206A pdb=" N LEU e 304 " --> pdb=" O ALA d 510 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER d 512 " --> pdb=" O LYS e 302 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS e 302 " --> pdb=" O SER d 512 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL e 301 " --> pdb=" O ILE e 496 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP e 498 " --> pdb=" O VAL e 301 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL e 303 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 542 through 546 removed outlier: 7.015A pdb=" N LEU d 543 " --> pdb=" O ILE d 555 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE d 555 " --> pdb=" O LEU d 543 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N HIS d 545 " --> pdb=" O THR d 553 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 26 through 29 removed outlier: 3.539A pdb=" N ASP e 240 " --> pdb=" O ASN e 235 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN e 250 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 222 through 224 removed outlier: 3.604A pdb=" N LEU e 255 " --> pdb=" O VAL e 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 261 through 262 Processing sheet with id=AC7, first strand: chain 'e' and resid 508 through 514 removed outlier: 3.797A pdb=" N TYR e 508 " --> pdb=" O GLY f 306 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU f 304 " --> pdb=" O ALA e 510 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER e 512 " --> pdb=" O LYS f 302 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS f 302 " --> pdb=" O SER e 512 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL f 301 " --> pdb=" O ILE f 496 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASP f 498 " --> pdb=" O VAL f 301 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL f 303 " --> pdb=" O ASP f 498 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 542 through 546 removed outlier: 4.361A pdb=" N SER e 554 " --> pdb=" O HIS e 545 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 26 through 29 Processing sheet with id=AD1, first strand: chain 'f' and resid 222 through 224 removed outlier: 3.654A pdb=" N LEU f 255 " --> pdb=" O VAL f 170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 261 through 262 Processing sheet with id=AD3, first strand: chain 'f' and resid 508 through 512 removed outlier: 7.302A pdb=" N LEU g 304 " --> pdb=" O ALA f 510 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER f 512 " --> pdb=" O LYS g 302 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS g 302 " --> pdb=" O SER f 512 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL g 301 " --> pdb=" O ILE g 496 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ASP g 498 " --> pdb=" O VAL g 301 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL g 303 " --> pdb=" O ASP g 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'f' and resid 542 through 546 removed outlier: 7.211A pdb=" N LEU f 543 " --> pdb=" O ILE f 555 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE f 555 " --> pdb=" O LEU f 543 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N HIS f 545 " --> pdb=" O THR f 553 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'g' and resid 26 through 29 removed outlier: 3.528A pdb=" N ASP g 240 " --> pdb=" O ASN g 235 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'g' and resid 222 through 224 removed outlier: 3.676A pdb=" N LEU g 255 " --> pdb=" O VAL g 170 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 261 through 263 removed outlier: 4.110A pdb=" N ARG g 266 " --> pdb=" O THR g 263 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 507 through 514 removed outlier: 6.542A pdb=" N LEU h 304 " --> pdb=" O ALA g 510 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER g 512 " --> pdb=" O LYS h 302 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS h 302 " --> pdb=" O SER g 512 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL h 301 " --> pdb=" O ILE h 496 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP h 498 " --> pdb=" O VAL h 301 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL h 303 " --> pdb=" O ASP h 498 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 542 through 546 removed outlier: 4.285A pdb=" N SER g 554 " --> pdb=" O HIS g 545 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'h' and resid 26 through 29 removed outlier: 3.581A pdb=" N ASP h 240 " --> pdb=" O ASN h 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'h' and resid 222 through 224 Processing sheet with id=AE3, first strand: chain 'h' and resid 261 through 263 removed outlier: 3.856A pdb=" N THR h 263 " --> pdb=" O ARG h 266 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG h 266 " --> pdb=" O THR h 263 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'h' and resid 508 through 514 removed outlier: 3.585A pdb=" N TYR h 508 " --> pdb=" O GLY i 306 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU i 304 " --> pdb=" O ALA h 510 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER h 512 " --> pdb=" O LYS i 302 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS i 302 " --> pdb=" O SER h 512 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL i 301 " --> pdb=" O ILE i 496 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASP i 498 " --> pdb=" O VAL i 301 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL i 303 " --> pdb=" O ASP i 498 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'h' and resid 542 through 543 removed outlier: 3.824A pdb=" N LEU h 543 " --> pdb=" O SER h 556 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'i' and resid 26 through 29 removed outlier: 3.571A pdb=" N ASP i 240 " --> pdb=" O ASN i 235 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'i' and resid 222 through 224 Processing sheet with id=AE8, first strand: chain 'i' and resid 261 through 262 removed outlier: 3.543A pdb=" N LEU i 261 " --> pdb=" O VAL i 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'i' and resid 508 through 514 removed outlier: 5.811A pdb=" N VAL i 509 " --> pdb=" O GLY j 306 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY j 306 " --> pdb=" O VAL i 509 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN i 511 " --> pdb=" O LEU j 304 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL j 301 " --> pdb=" O ILE j 496 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASP j 498 " --> pdb=" O VAL j 301 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL j 303 " --> pdb=" O ASP j 498 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'i' and resid 542 through 546 removed outlier: 4.446A pdb=" N SER i 554 " --> pdb=" O HIS i 545 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'j' and resid 26 through 29 removed outlier: 3.546A pdb=" N ASP j 240 " --> pdb=" O ASN j 235 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN j 250 " --> pdb=" O ASP j 245 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 222 through 224 Processing sheet with id=AF4, first strand: chain 'j' and resid 261 through 262 Processing sheet with id=AF5, first strand: chain 'j' and resid 508 through 514 removed outlier: 7.028A pdb=" N LEU k 304 " --> pdb=" O ALA j 510 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER j 512 " --> pdb=" O LYS k 302 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS k 302 " --> pdb=" O SER j 512 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL k 301 " --> pdb=" O ILE k 496 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP k 498 " --> pdb=" O VAL k 301 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL k 303 " --> pdb=" O ASP k 498 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'j' and resid 543 through 546 removed outlier: 3.514A pdb=" N LEU j 543 " --> pdb=" O SER j 556 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS j 545 " --> pdb=" O SER j 554 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER j 554 " --> pdb=" O HIS j 545 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'k' and resid 26 through 29 removed outlier: 3.720A pdb=" N GLN k 250 " --> pdb=" O ASP k 245 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'k' and resid 222 through 224 Processing sheet with id=AF9, first strand: chain 'k' and resid 261 through 262 Processing sheet with id=AG1, first strand: chain 'k' and resid 508 through 514 removed outlier: 3.834A pdb=" N TYR k 508 " --> pdb=" O GLY l 306 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU l 304 " --> pdb=" O ALA k 510 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER k 512 " --> pdb=" O LYS l 302 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS l 302 " --> pdb=" O SER k 512 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL l 301 " --> pdb=" O ILE l 496 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP l 498 " --> pdb=" O VAL l 301 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL l 303 " --> pdb=" O ASP l 498 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 543 through 546 Processing sheet with id=AG3, first strand: chain 'l' and resid 26 through 29 Processing sheet with id=AG4, first strand: chain 'l' and resid 222 through 224 removed outlier: 3.700A pdb=" N LEU l 255 " --> pdb=" O VAL l 170 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'l' and resid 261 through 262 Processing sheet with id=AG6, first strand: chain 'l' and resid 542 through 543 2314 hydrogen bonds defined for protein. 6732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13127 1.34 - 1.46: 5852 1.46 - 1.57: 21533 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 40644 Sorted by residual: bond pdb=" CA GLY d 209 " pdb=" C GLY d 209 " ideal model delta sigma weight residual 1.511 1.521 -0.010 6.90e-03 2.10e+04 2.30e+00 bond pdb=" C HIS d 31 " pdb=" N PRO d 32 " ideal model delta sigma weight residual 1.337 1.350 -0.013 9.80e-03 1.04e+04 1.78e+00 bond pdb=" CA GLY l 264 " pdb=" C GLY l 264 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.46e+00 bond pdb=" C ALA d 208 " pdb=" N GLY d 209 " ideal model delta sigma weight residual 1.340 1.332 0.008 6.60e-03 2.30e+04 1.41e+00 bond pdb=" N GLY l 264 " pdb=" CA GLY l 264 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.04e+00 ... (remaining 40639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 55212 4.98 - 9.96: 61 9.96 - 14.94: 0 14.94 - 19.92: 0 19.92 - 24.90: 11 Bond angle restraints: 55284 Sorted by residual: angle pdb=" O HIS i 515 " pdb=" C HIS i 515 " pdb=" N PRO i 516 " ideal model delta sigma weight residual 121.23 97.76 23.47 7.00e-01 2.04e+00 1.12e+03 angle pdb=" O HIS l 515 " pdb=" C HIS l 515 " pdb=" N PRO l 516 " ideal model delta sigma weight residual 121.23 98.62 22.61 7.00e-01 2.04e+00 1.04e+03 angle pdb=" O HIS f 515 " pdb=" C HIS f 515 " pdb=" N PRO f 516 " ideal model delta sigma weight residual 121.23 99.28 21.95 7.00e-01 2.04e+00 9.83e+02 angle pdb=" O HIS d 515 " pdb=" C HIS d 515 " pdb=" N PRO d 516 " ideal model delta sigma weight residual 121.23 99.61 21.62 7.00e-01 2.04e+00 9.54e+02 angle pdb=" O HIS c 515 " pdb=" C HIS c 515 " pdb=" N PRO c 516 " ideal model delta sigma weight residual 121.17 96.27 24.90 8.50e-01 1.38e+00 8.58e+02 ... (remaining 55279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 21580 17.99 - 35.98: 1975 35.98 - 53.97: 314 53.97 - 71.96: 45 71.96 - 89.95: 26 Dihedral angle restraints: 23940 sinusoidal: 9564 harmonic: 14376 Sorted by residual: dihedral pdb=" CA PHE c 188 " pdb=" C PHE c 188 " pdb=" N LEU c 189 " pdb=" CA LEU c 189 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA GLU l 552 " pdb=" C GLU l 552 " pdb=" N THR l 553 " pdb=" CA THR l 553 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE f 188 " pdb=" C PHE f 188 " pdb=" N LEU f 189 " pdb=" CA LEU f 189 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 23937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3738 0.030 - 0.060: 1564 0.060 - 0.089: 425 0.089 - 0.119: 289 0.119 - 0.149: 32 Chirality restraints: 6048 Sorted by residual: chirality pdb=" CA ASP l 162 " pdb=" N ASP l 162 " pdb=" C ASP l 162 " pdb=" CB ASP l 162 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ASP c 162 " pdb=" N ASP c 162 " pdb=" C ASP c 162 " pdb=" CB ASP c 162 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ASN k 129 " pdb=" N ASN k 129 " pdb=" C ASN k 129 " pdb=" CB ASN k 129 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 6045 not shown) Planarity restraints: 7176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS c 515 " -0.103 2.00e-02 2.50e+03 1.75e-01 3.07e+02 pdb=" C HIS c 515 " 0.303 2.00e-02 2.50e+03 pdb=" O HIS c 515 " -0.108 2.00e-02 2.50e+03 pdb=" N PRO c 516 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS a 515 " -0.101 2.00e-02 2.50e+03 1.74e-01 3.02e+02 pdb=" C HIS a 515 " 0.301 2.00e-02 2.50e+03 pdb=" O HIS a 515 " -0.107 2.00e-02 2.50e+03 pdb=" N PRO a 516 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS i 515 " -0.099 2.00e-02 2.50e+03 1.70e-01 2.88e+02 pdb=" C HIS i 515 " 0.294 2.00e-02 2.50e+03 pdb=" O HIS i 515 " -0.105 2.00e-02 2.50e+03 pdb=" N PRO i 516 " -0.090 2.00e-02 2.50e+03 ... (remaining 7173 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 16639 2.94 - 3.43: 43348 3.43 - 3.92: 63992 3.92 - 4.41: 69223 4.41 - 4.90: 113489 Nonbonded interactions: 306691 Sorted by model distance: nonbonded pdb=" O ALA a 199 " pdb=" OE1 GLU a 203 " model vdw 2.449 3.040 nonbonded pdb=" O HIS a 515 " pdb=" CA PRO a 516 " model vdw 2.453 2.776 nonbonded pdb=" O HIS g 515 " pdb=" CA PRO g 516 " model vdw 2.458 2.776 nonbonded pdb=" O HIS c 515 " pdb=" CA PRO c 516 " model vdw 2.477 2.776 nonbonded pdb=" O HIS i 515 " pdb=" CA PRO i 516 " model vdw 2.491 2.776 ... (remaining 306686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.710 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.002 0.025 40644 Z= 0.110 Angle : 0.618 24.899 55284 Z= 0.466 Chirality : 0.040 0.149 6048 Planarity : 0.008 0.175 7176 Dihedral : 13.850 89.952 14700 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.12), residues: 4920 helix: 2.48 (0.10), residues: 2772 sheet: 0.78 (0.24), residues: 420 loop : -1.25 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 604 TYR 0.023 0.001 TYR b 108 PHE 0.026 0.001 PHE f 124 TRP 0.030 0.002 TRP j 258 HIS 0.005 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00225 (40644) covalent geometry : angle 0.61773 (55284) hydrogen bonds : bond 0.15123 ( 2314) hydrogen bonds : angle 5.26609 ( 6732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1225 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8195 (mt-10) REVERT: a 70 GLN cc_start: 0.9193 (mt0) cc_final: 0.8719 (mt0) REVERT: a 160 TYR cc_start: 0.9105 (t80) cc_final: 0.8897 (t80) REVERT: a 170 VAL cc_start: 0.9721 (t) cc_final: 0.9499 (m) REVERT: a 212 PHE cc_start: 0.9112 (m-10) cc_final: 0.8762 (m-80) REVERT: a 300 SER cc_start: 0.8719 (m) cc_final: 0.8356 (m) REVERT: a 571 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8332 (mm-30) REVERT: a 600 PHE cc_start: 0.8309 (t80) cc_final: 0.7963 (t80) REVERT: b 91 LEU cc_start: 0.9077 (mm) cc_final: 0.8811 (pp) REVERT: b 129 ASN cc_start: 0.8976 (t0) cc_final: 0.8564 (t0) REVERT: b 170 VAL cc_start: 0.9725 (t) cc_final: 0.9474 (m) REVERT: b 548 ASN cc_start: 0.8140 (p0) cc_final: 0.7424 (m-40) REVERT: b 600 PHE cc_start: 0.8434 (t80) cc_final: 0.8168 (t80) REVERT: c 70 GLN cc_start: 0.9321 (mt0) cc_final: 0.8894 (mt0) REVERT: c 90 TRP cc_start: 0.8056 (t-100) cc_final: 0.6237 (t-100) REVERT: c 124 PHE cc_start: 0.8450 (t80) cc_final: 0.7976 (t80) REVERT: c 142 LEU cc_start: 0.9377 (mt) cc_final: 0.9151 (mt) REVERT: c 160 TYR cc_start: 0.9165 (t80) cc_final: 0.8741 (t80) REVERT: c 261 LEU cc_start: 0.8681 (tp) cc_final: 0.8350 (mp) REVERT: c 511 ASN cc_start: 0.8759 (t0) cc_final: 0.8543 (t0) REVERT: d 63 GLU cc_start: 0.8525 (tp30) cc_final: 0.8126 (tp30) REVERT: d 79 ASN cc_start: 0.8957 (m-40) cc_final: 0.8512 (p0) REVERT: d 129 ASN cc_start: 0.9168 (p0) cc_final: 0.8411 (p0) REVERT: d 170 VAL cc_start: 0.9685 (t) cc_final: 0.9410 (m) REVERT: d 511 ASN cc_start: 0.8658 (t0) cc_final: 0.8115 (t0) REVERT: d 513 PHE cc_start: 0.8639 (m-80) cc_final: 0.7878 (m-80) REVERT: d 547 ASN cc_start: 0.7345 (t0) cc_final: 0.6963 (p0) REVERT: d 600 PHE cc_start: 0.8337 (t80) cc_final: 0.8117 (t80) REVERT: d 611 ASP cc_start: 0.8194 (m-30) cc_final: 0.7939 (m-30) REVERT: d 615 LEU cc_start: 0.8854 (pp) cc_final: 0.8515 (tp) REVERT: e 79 ASN cc_start: 0.8944 (m-40) cc_final: 0.8625 (p0) REVERT: e 90 TRP cc_start: 0.8359 (t-100) cc_final: 0.7628 (t-100) REVERT: e 100 GLN cc_start: 0.8482 (mt0) cc_final: 0.8204 (mp10) REVERT: e 125 ASP cc_start: 0.9051 (t0) cc_final: 0.8690 (m-30) REVERT: e 160 TYR cc_start: 0.9113 (t80) cc_final: 0.8874 (t80) REVERT: e 236 HIS cc_start: 0.7915 (p90) cc_final: 0.7681 (p-80) REVERT: e 304 LEU cc_start: 0.8725 (pp) cc_final: 0.8457 (pp) REVERT: e 548 ASN cc_start: 0.8537 (p0) cc_final: 0.8112 (m-40) REVERT: e 600 PHE cc_start: 0.8440 (t80) cc_final: 0.8182 (t80) REVERT: f 70 GLN cc_start: 0.9071 (mt0) cc_final: 0.8683 (mt0) REVERT: f 79 ASN cc_start: 0.9234 (m110) cc_final: 0.8884 (p0) REVERT: f 91 LEU cc_start: 0.8603 (mm) cc_final: 0.8327 (pp) REVERT: f 124 PHE cc_start: 0.6540 (p90) cc_final: 0.6232 (p90) REVERT: f 160 TYR cc_start: 0.9006 (t80) cc_final: 0.8760 (t80) REVERT: f 548 ASN cc_start: 0.7327 (m110) cc_final: 0.6992 (p0) REVERT: f 608 TYR cc_start: 0.8637 (m-10) cc_final: 0.8275 (m-10) REVERT: g 79 ASN cc_start: 0.8832 (m-40) cc_final: 0.8491 (p0) REVERT: g 83 TYR cc_start: 0.8070 (t80) cc_final: 0.7642 (t80) REVERT: g 90 TRP cc_start: 0.8304 (t-100) cc_final: 0.7303 (t-100) REVERT: g 127 TRP cc_start: 0.8872 (t-100) cc_final: 0.8406 (t60) REVERT: g 237 ARG cc_start: 0.7982 (ptt-90) cc_final: 0.7544 (ttp-110) REVERT: g 261 LEU cc_start: 0.8998 (tt) cc_final: 0.8603 (mp) REVERT: g 600 PHE cc_start: 0.8817 (t80) cc_final: 0.8493 (t80) REVERT: h 63 GLU cc_start: 0.8307 (tp30) cc_final: 0.7984 (tp30) REVERT: h 70 GLN cc_start: 0.9204 (mt0) cc_final: 0.8950 (mt0) REVERT: h 79 ASN cc_start: 0.8984 (m110) cc_final: 0.8496 (p0) REVERT: h 91 LEU cc_start: 0.9037 (tp) cc_final: 0.8763 (pp) REVERT: h 160 TYR cc_start: 0.8958 (t80) cc_final: 0.8717 (t80) REVERT: h 212 PHE cc_start: 0.9179 (m-10) cc_final: 0.8769 (m-80) REVERT: h 261 LEU cc_start: 0.8699 (tt) cc_final: 0.8347 (mt) REVERT: h 511 ASN cc_start: 0.9025 (t0) cc_final: 0.8595 (t0) REVERT: h 513 PHE cc_start: 0.8463 (m-80) cc_final: 0.8137 (m-80) REVERT: h 548 ASN cc_start: 0.7090 (m110) cc_final: 0.6884 (p0) REVERT: h 612 ILE cc_start: 0.9221 (mm) cc_final: 0.8638 (mm) REVERT: h 615 LEU cc_start: 0.8592 (pp) cc_final: 0.8166 (tp) REVERT: i 70 GLN cc_start: 0.9393 (mt0) cc_final: 0.9152 (mt0) REVERT: i 160 TYR cc_start: 0.9040 (t80) cc_final: 0.8530 (t80) REVERT: i 297 ASN cc_start: 0.8479 (t0) cc_final: 0.8247 (t0) REVERT: i 304 LEU cc_start: 0.9145 (pp) cc_final: 0.8923 (pp) REVERT: i 511 ASN cc_start: 0.8730 (t0) cc_final: 0.8174 (t0) REVERT: i 513 PHE cc_start: 0.8459 (m-80) cc_final: 0.7890 (m-80) REVERT: i 548 ASN cc_start: 0.7301 (m110) cc_final: 0.6995 (p0) REVERT: j 63 GLU cc_start: 0.8042 (tp30) cc_final: 0.7840 (tp30) REVERT: j 70 GLN cc_start: 0.9184 (mt0) cc_final: 0.8818 (mt0) REVERT: j 125 ASP cc_start: 0.9092 (t70) cc_final: 0.8634 (m-30) REVERT: j 142 LEU cc_start: 0.9470 (mt) cc_final: 0.9170 (mt) REVERT: j 170 VAL cc_start: 0.9752 (t) cc_final: 0.9516 (p) REVERT: j 271 SER cc_start: 0.9520 (p) cc_final: 0.9270 (m) REVERT: j 304 LEU cc_start: 0.8739 (pp) cc_final: 0.8467 (pp) REVERT: k 57 ASN cc_start: 0.8866 (m-40) cc_final: 0.8585 (m110) REVERT: k 261 LEU cc_start: 0.9013 (tp) cc_final: 0.8731 (mt) REVERT: k 535 GLU cc_start: 0.8237 (tp30) cc_final: 0.7742 (tp30) REVERT: k 571 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8381 (mm-30) REVERT: l 70 GLN cc_start: 0.9162 (mt0) cc_final: 0.8686 (mt0) REVERT: l 79 ASN cc_start: 0.9143 (m110) cc_final: 0.8751 (p0) REVERT: l 160 TYR cc_start: 0.8954 (t80) cc_final: 0.8694 (t80) REVERT: l 511 ASN cc_start: 0.7781 (m110) cc_final: 0.7570 (m-40) outliers start: 0 outliers final: 0 residues processed: 1225 average time/residue: 0.2335 time to fit residues: 452.6029 Evaluate side-chains 755 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 9.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 289 HIS ** a 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 511 ASN b 549 GLN c 192 HIS c 274 GLN ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 621 GLN ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 102 GLN ** i 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 551 GLN k 44 HIS ** k 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.080906 restraints weight = 96004.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.083086 restraints weight = 60205.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084476 restraints weight = 45074.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.085330 restraints weight = 37811.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085786 restraints weight = 34035.908| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40644 Z= 0.207 Angle : 0.647 7.421 55284 Z= 0.335 Chirality : 0.042 0.161 6048 Planarity : 0.005 0.070 7176 Dihedral : 4.430 22.836 5580 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.12 % Allowed : 4.86 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.12), residues: 4920 helix: 2.34 (0.10), residues: 2784 sheet: 0.18 (0.22), residues: 564 loop : -1.23 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG d 128 TYR 0.031 0.002 TYR b 108 PHE 0.023 0.002 PHE c 124 TRP 0.034 0.003 TRP l 127 HIS 0.009 0.001 HIS i 93 Details of bonding type rmsd covalent geometry : bond 0.00473 (40644) covalent geometry : angle 0.64664 (55284) hydrogen bonds : bond 0.04278 ( 2314) hydrogen bonds : angle 4.40933 ( 6732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 914 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8304 (mt-10) REVERT: a 129 ASN cc_start: 0.8990 (t0) cc_final: 0.8746 (p0) REVERT: a 212 PHE cc_start: 0.9145 (m-10) cc_final: 0.8678 (m-80) REVERT: a 231 TYR cc_start: 0.7887 (m-10) cc_final: 0.7437 (m-80) REVERT: a 600 PHE cc_start: 0.8293 (t80) cc_final: 0.7959 (t80) REVERT: b 70 GLN cc_start: 0.9371 (mt0) cc_final: 0.8986 (mt0) REVERT: b 128 ARG cc_start: 0.9066 (mtt180) cc_final: 0.8574 (mmt90) REVERT: b 142 LEU cc_start: 0.9576 (mt) cc_final: 0.9353 (mt) REVERT: b 170 VAL cc_start: 0.9717 (t) cc_final: 0.9479 (m) REVERT: b 548 ASN cc_start: 0.8196 (p0) cc_final: 0.7477 (m-40) REVERT: b 600 PHE cc_start: 0.8347 (t80) cc_final: 0.8132 (t80) REVERT: c 70 GLN cc_start: 0.9348 (mt0) cc_final: 0.8978 (mt0) REVERT: c 83 TYR cc_start: 0.8215 (t80) cc_final: 0.7624 (t80) REVERT: c 127 TRP cc_start: 0.8275 (t60) cc_final: 0.7762 (t60) REVERT: c 160 TYR cc_start: 0.9349 (t80) cc_final: 0.8878 (t80) REVERT: c 170 VAL cc_start: 0.9791 (m) cc_final: 0.9588 (m) REVERT: c 304 LEU cc_start: 0.9002 (pp) cc_final: 0.8765 (pp) REVERT: c 511 ASN cc_start: 0.8956 (t0) cc_final: 0.8717 (t0) REVERT: d 63 GLU cc_start: 0.8485 (tp30) cc_final: 0.8198 (tp30) REVERT: d 79 ASN cc_start: 0.9053 (m-40) cc_final: 0.8610 (p0) REVERT: d 136 LEU cc_start: 0.9402 (tp) cc_final: 0.8718 (tt) REVERT: d 159 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8315 (mtmt) REVERT: d 226 ASP cc_start: 0.8167 (m-30) cc_final: 0.7957 (m-30) REVERT: d 511 ASN cc_start: 0.8935 (t0) cc_final: 0.8472 (t0) REVERT: d 517 TYR cc_start: 0.8943 (t80) cc_final: 0.8476 (t80) REVERT: d 547 ASN cc_start: 0.7281 (t0) cc_final: 0.6837 (p0) REVERT: d 611 ASP cc_start: 0.8491 (m-30) cc_final: 0.7610 (m-30) REVERT: d 615 LEU cc_start: 0.8892 (pp) cc_final: 0.8598 (tp) REVERT: d 616 PHE cc_start: 0.8380 (t80) cc_final: 0.8109 (t80) REVERT: e 79 ASN cc_start: 0.8951 (m-40) cc_final: 0.8591 (p0) REVERT: e 100 GLN cc_start: 0.8472 (mt0) cc_final: 0.8205 (mp10) REVERT: e 125 ASP cc_start: 0.8942 (t0) cc_final: 0.8486 (m-30) REVERT: e 511 ASN cc_start: 0.8675 (t0) cc_final: 0.8423 (t0) REVERT: e 548 ASN cc_start: 0.8601 (p0) cc_final: 0.8087 (m-40) REVERT: f 91 LEU cc_start: 0.8907 (mm) cc_final: 0.8477 (pp) REVERT: f 137 ASP cc_start: 0.9310 (m-30) cc_final: 0.9094 (m-30) REVERT: f 160 TYR cc_start: 0.9298 (t80) cc_final: 0.9060 (t80) REVERT: f 548 ASN cc_start: 0.7457 (m110) cc_final: 0.7119 (p0) REVERT: f 574 LEU cc_start: 0.9322 (tp) cc_final: 0.9092 (tp) REVERT: g 41 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8329 (mt-10) REVERT: g 79 ASN cc_start: 0.8968 (m-40) cc_final: 0.8583 (p0) REVERT: g 600 PHE cc_start: 0.8882 (t80) cc_final: 0.8299 (t80) REVERT: g 608 TYR cc_start: 0.8605 (m-10) cc_final: 0.8182 (m-10) REVERT: h 63 GLU cc_start: 0.8433 (tp30) cc_final: 0.8077 (tp30) REVERT: h 70 GLN cc_start: 0.9143 (mt0) cc_final: 0.8875 (mt0) REVERT: h 79 ASN cc_start: 0.8961 (m110) cc_final: 0.8519 (p0) REVERT: h 142 LEU cc_start: 0.9391 (mt) cc_final: 0.9191 (mt) REVERT: h 160 TYR cc_start: 0.9234 (t80) cc_final: 0.9016 (t80) REVERT: h 307 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7477 (tmm-80) REVERT: h 511 ASN cc_start: 0.9330 (t0) cc_final: 0.8898 (t0) REVERT: i 70 GLN cc_start: 0.9346 (mt0) cc_final: 0.9107 (mt0) REVERT: i 160 TYR cc_start: 0.9171 (t80) cc_final: 0.8741 (t80) REVERT: i 511 ASN cc_start: 0.9352 (t0) cc_final: 0.8374 (t0) REVERT: i 513 PHE cc_start: 0.8506 (m-80) cc_final: 0.7850 (m-80) REVERT: i 548 ASN cc_start: 0.7569 (m110) cc_final: 0.7129 (p0) REVERT: j 63 GLU cc_start: 0.8254 (tp30) cc_final: 0.7997 (tp30) REVERT: j 70 GLN cc_start: 0.9236 (mt0) cc_final: 0.8920 (mt0) REVERT: j 125 ASP cc_start: 0.9076 (t70) cc_final: 0.8642 (m-30) REVERT: j 142 LEU cc_start: 0.9406 (mt) cc_final: 0.9150 (mt) REVERT: j 159 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8920 (mtmt) REVERT: j 200 THR cc_start: 0.8915 (m) cc_final: 0.8601 (p) REVERT: j 304 LEU cc_start: 0.9130 (pp) cc_final: 0.8886 (pp) REVERT: k 159 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8784 (mtmt) REVERT: k 262 TRP cc_start: 0.8594 (t-100) cc_final: 0.8254 (t-100) REVERT: k 499 VAL cc_start: 0.8993 (t) cc_final: 0.8734 (p) REVERT: k 535 GLU cc_start: 0.8601 (tp30) cc_final: 0.8093 (tp30) REVERT: l 79 ASN cc_start: 0.9001 (m110) cc_final: 0.8631 (p0) REVERT: l 160 TYR cc_start: 0.9239 (t80) cc_final: 0.8763 (t80) REVERT: l 261 LEU cc_start: 0.8978 (tp) cc_final: 0.8748 (tt) REVERT: l 302 LYS cc_start: 0.9380 (mppt) cc_final: 0.9100 (mppt) REVERT: l 610 THR cc_start: 0.9564 (p) cc_final: 0.9298 (p) outliers start: 5 outliers final: 0 residues processed: 917 average time/residue: 0.2369 time to fit residues: 342.6719 Evaluate side-chains 674 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 368 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 476 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 245 optimal weight: 20.0000 chunk 400 optimal weight: 0.9980 chunk 396 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 75 HIS ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 515 HIS ** a 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 250 GLN b 511 ASN b 549 GLN d 70 GLN ** d 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 621 GLN d 622 HIS ** e 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 515 HIS ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 515 HIS ** i 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 515 HIS k 102 GLN ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 236 HIS k 297 ASN l 192 HIS l 551 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084109 restraints weight = 95626.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086421 restraints weight = 58192.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087882 restraints weight = 42763.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088750 restraints weight = 35483.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089300 restraints weight = 31835.680| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40644 Z= 0.128 Angle : 0.589 8.372 55284 Z= 0.301 Chirality : 0.041 0.184 6048 Planarity : 0.004 0.067 7176 Dihedral : 4.312 20.787 5580 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.21 % 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: 1.57 (0.12), residues: 4920 helix: 2.38 (0.10), residues: 2784 sheet: 0.35 (0.22), residues: 564 loop : -1.23 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 530 TYR 0.025 0.001 TYR a 608 PHE 0.028 0.001 PHE f 157 TRP 0.055 0.002 TRP l 127 HIS 0.016 0.001 HIS j 515 Details of bonding type rmsd covalent geometry : bond 0.00285 (40644) covalent geometry : angle 0.58874 (55284) hydrogen bonds : bond 0.03864 ( 2314) hydrogen bonds : angle 4.14673 ( 6732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 913 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 41 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8303 (mt-10) REVERT: a 129 ASN cc_start: 0.9076 (t0) cc_final: 0.8839 (p0) REVERT: a 212 PHE cc_start: 0.9173 (m-10) cc_final: 0.8712 (m-80) REVERT: a 297 ASN cc_start: 0.8996 (t0) cc_final: 0.8696 (t0) REVERT: a 304 LEU cc_start: 0.9163 (pt) cc_final: 0.8836 (pp) REVERT: a 600 PHE cc_start: 0.8334 (t80) cc_final: 0.8099 (t80) REVERT: b 70 GLN cc_start: 0.9353 (mt0) cc_final: 0.9040 (mt0) REVERT: b 127 TRP cc_start: 0.8805 (t-100) cc_final: 0.8346 (t-100) REVERT: b 128 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8473 (mmt90) REVERT: b 142 LEU cc_start: 0.9573 (mt) cc_final: 0.9350 (mt) REVERT: b 170 VAL cc_start: 0.9663 (t) cc_final: 0.9240 (p) REVERT: b 511 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8420 (m-40) REVERT: b 548 ASN cc_start: 0.8297 (p0) cc_final: 0.7489 (m-40) REVERT: b 600 PHE cc_start: 0.8318 (t80) cc_final: 0.8007 (t80) REVERT: c 70 GLN cc_start: 0.9282 (mt0) cc_final: 0.8848 (mt0) REVERT: c 127 TRP cc_start: 0.8179 (t60) cc_final: 0.7618 (t60) REVERT: c 160 TYR cc_start: 0.9339 (t80) cc_final: 0.8868 (t80) REVERT: c 170 VAL cc_start: 0.9751 (m) cc_final: 0.9539 (m) REVERT: c 511 ASN cc_start: 0.8980 (t0) cc_final: 0.8722 (t0) REVERT: d 63 GLU cc_start: 0.8358 (tp30) cc_final: 0.8137 (tp30) REVERT: d 79 ASN cc_start: 0.8905 (m-40) cc_final: 0.8528 (p0) REVERT: d 127 TRP cc_start: 0.8531 (t-100) cc_final: 0.8192 (t-100) REVERT: d 136 LEU cc_start: 0.9380 (tp) cc_final: 0.8705 (tt) REVERT: d 159 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8150 (mtmt) REVERT: d 511 ASN cc_start: 0.8856 (t0) cc_final: 0.8524 (t0) REVERT: d 547 ASN cc_start: 0.7289 (t0) cc_final: 0.6891 (p0) REVERT: d 611 ASP cc_start: 0.8336 (m-30) cc_final: 0.7470 (m-30) REVERT: d 615 LEU cc_start: 0.8884 (pp) cc_final: 0.8566 (tp) REVERT: e 79 ASN cc_start: 0.8911 (m-40) cc_final: 0.8587 (p0) REVERT: e 100 GLN cc_start: 0.8474 (mt0) cc_final: 0.8226 (mp10) REVERT: e 125 ASP cc_start: 0.8957 (t0) cc_final: 0.8614 (m-30) REVERT: e 127 TRP cc_start: 0.8711 (t-100) cc_final: 0.8314 (t-100) REVERT: e 214 GLU cc_start: 0.9003 (pp20) cc_final: 0.8782 (pp20) REVERT: e 511 ASN cc_start: 0.8615 (t0) cc_final: 0.8390 (t0) REVERT: e 548 ASN cc_start: 0.8581 (p0) cc_final: 0.8072 (m-40) REVERT: f 79 ASN cc_start: 0.9102 (m110) cc_final: 0.8617 (p0) REVERT: f 91 LEU cc_start: 0.8822 (mm) cc_final: 0.8378 (pp) REVERT: f 548 ASN cc_start: 0.7398 (m110) cc_final: 0.7117 (p0) REVERT: g 41 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8294 (mt-10) REVERT: g 79 ASN cc_start: 0.8975 (m-40) cc_final: 0.8473 (p0) REVERT: g 127 TRP cc_start: 0.8593 (t-100) cc_final: 0.8303 (t-100) REVERT: g 237 ARG cc_start: 0.7946 (ptt-90) cc_final: 0.7658 (ttp-110) REVERT: g 548 ASN cc_start: 0.8284 (p0) cc_final: 0.7483 (t0) REVERT: g 600 PHE cc_start: 0.8818 (t80) cc_final: 0.8439 (t80) REVERT: g 608 TYR cc_start: 0.8601 (m-10) cc_final: 0.8206 (m-10) REVERT: h 63 GLU cc_start: 0.8433 (tp30) cc_final: 0.8023 (tp30) REVERT: h 79 ASN cc_start: 0.8894 (m110) cc_final: 0.8449 (p0) REVERT: h 307 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.7319 (tmm-80) REVERT: h 511 ASN cc_start: 0.9170 (t0) cc_final: 0.8836 (t0) REVERT: i 63 GLU cc_start: 0.8432 (tp30) cc_final: 0.7954 (tp30) REVERT: i 70 GLN cc_start: 0.9304 (mt0) cc_final: 0.9020 (mt0) REVERT: i 127 TRP cc_start: 0.8528 (t-100) cc_final: 0.8302 (t-100) REVERT: i 160 TYR cc_start: 0.9143 (t80) cc_final: 0.8745 (t80) REVERT: i 304 LEU cc_start: 0.9169 (pp) cc_final: 0.8950 (pp) REVERT: i 511 ASN cc_start: 0.9240 (t0) cc_final: 0.8200 (t0) REVERT: i 513 PHE cc_start: 0.8494 (m-80) cc_final: 0.7768 (m-80) REVERT: i 548 ASN cc_start: 0.7562 (m110) cc_final: 0.7087 (p0) REVERT: i 601 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8828 (mmmm) REVERT: i 608 TYR cc_start: 0.8818 (m-10) cc_final: 0.8002 (m-10) REVERT: j 63 GLU cc_start: 0.8160 (tp30) cc_final: 0.7908 (tp30) REVERT: j 70 GLN cc_start: 0.9164 (mt0) cc_final: 0.8845 (mt0) REVERT: j 125 ASP cc_start: 0.9101 (t70) cc_final: 0.8639 (m-30) REVERT: j 142 LEU cc_start: 0.9367 (mt) cc_final: 0.9167 (mt) REVERT: j 159 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8833 (mtmt) REVERT: j 200 THR cc_start: 0.8914 (m) cc_final: 0.8648 (p) REVERT: j 304 LEU cc_start: 0.9051 (pp) cc_final: 0.8796 (pp) REVERT: k 262 TRP cc_start: 0.8594 (t-100) cc_final: 0.8359 (t-100) REVERT: k 535 GLU cc_start: 0.8568 (tp30) cc_final: 0.8036 (tp30) REVERT: l 79 ASN cc_start: 0.8996 (m110) cc_final: 0.8657 (p0) REVERT: l 160 TYR cc_start: 0.9235 (t80) cc_final: 0.8777 (t80) REVERT: l 245 ASP cc_start: 0.9153 (t0) cc_final: 0.8941 (t0) REVERT: l 265 ASP cc_start: 0.7994 (p0) cc_final: 0.7669 (p0) REVERT: l 296 ARG cc_start: 0.7776 (tmm-80) cc_final: 0.7488 (tmm-80) REVERT: l 302 LYS cc_start: 0.9355 (mppt) cc_final: 0.9023 (mppt) outliers start: 4 outliers final: 0 residues processed: 915 average time/residue: 0.2305 time to fit residues: 332.2616 Evaluate side-chains 683 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 392 optimal weight: 5.9990 chunk 371 optimal weight: 3.9990 chunk 449 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 479 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 254 optimal weight: 0.0060 chunk 103 optimal weight: 1.9990 chunk 385 optimal weight: 7.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 515 HIS b 549 GLN ** d 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 GLN g 515 HIS h 297 ASN ** i 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 236 HIS ** i 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 236 HIS l 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083087 restraints weight = 96388.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.085395 restraints weight = 59222.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086821 restraints weight = 43710.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087746 restraints weight = 36370.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088216 restraints weight = 32577.755| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40644 Z= 0.147 Angle : 0.597 9.426 55284 Z= 0.305 Chirality : 0.041 0.152 6048 Planarity : 0.004 0.058 7176 Dihedral : 4.321 20.805 5580 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.12), residues: 4920 helix: 2.35 (0.10), residues: 2784 sheet: 0.29 (0.21), residues: 612 loop : -1.28 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG d 122 TYR 0.035 0.001 TYR c 108 PHE 0.027 0.001 PHE g 219 TRP 0.059 0.002 TRP l 127 HIS 0.013 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00334 (40644) covalent geometry : angle 0.59722 (55284) hydrogen bonds : bond 0.03770 ( 2314) hydrogen bonds : angle 4.10206 ( 6732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 885 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8339 (mt-10) REVERT: a 212 PHE cc_start: 0.9179 (m-10) cc_final: 0.8732 (m-80) REVERT: a 297 ASN cc_start: 0.8941 (t0) cc_final: 0.8593 (t0) REVERT: a 600 PHE cc_start: 0.8352 (t80) cc_final: 0.8151 (t80) REVERT: b 70 GLN cc_start: 0.9361 (mt0) cc_final: 0.9038 (mt0) REVERT: b 127 TRP cc_start: 0.8843 (t-100) cc_final: 0.8414 (t-100) REVERT: b 548 ASN cc_start: 0.8345 (p0) cc_final: 0.7558 (m-40) REVERT: c 70 GLN cc_start: 0.9260 (mt0) cc_final: 0.8916 (mt0) REVERT: c 127 TRP cc_start: 0.8212 (t60) cc_final: 0.7685 (t60) REVERT: c 160 TYR cc_start: 0.9362 (t80) cc_final: 0.8842 (t80) REVERT: c 511 ASN cc_start: 0.8991 (t0) cc_final: 0.8707 (t0) REVERT: c 608 TYR cc_start: 0.8495 (m-10) cc_final: 0.8234 (m-10) REVERT: d 63 GLU cc_start: 0.8405 (tp30) cc_final: 0.8078 (tp30) REVERT: d 79 ASN cc_start: 0.8898 (m-40) cc_final: 0.8529 (p0) REVERT: d 127 TRP cc_start: 0.8480 (t-100) cc_final: 0.8107 (t-100) REVERT: d 136 LEU cc_start: 0.9390 (tp) cc_final: 0.8732 (tt) REVERT: d 159 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8244 (mtmt) REVERT: d 203 GLU cc_start: 0.8359 (tt0) cc_final: 0.8074 (tt0) REVERT: d 226 ASP cc_start: 0.8146 (m-30) cc_final: 0.7930 (m-30) REVERT: d 511 ASN cc_start: 0.8836 (t0) cc_final: 0.8506 (t0) REVERT: d 517 TYR cc_start: 0.8952 (t80) cc_final: 0.8415 (t80) REVERT: d 547 ASN cc_start: 0.7349 (t0) cc_final: 0.6950 (p0) REVERT: d 611 ASP cc_start: 0.8361 (m-30) cc_final: 0.7531 (m-30) REVERT: d 615 LEU cc_start: 0.8898 (pp) cc_final: 0.8598 (tp) REVERT: e 79 ASN cc_start: 0.8852 (m-40) cc_final: 0.8554 (p0) REVERT: e 100 GLN cc_start: 0.8423 (mt0) cc_final: 0.8191 (mp10) REVERT: e 214 GLU cc_start: 0.9069 (pp20) cc_final: 0.8838 (pp20) REVERT: e 511 ASN cc_start: 0.8635 (t0) cc_final: 0.8336 (t0) REVERT: e 548 ASN cc_start: 0.8588 (p0) cc_final: 0.8043 (m110) REVERT: f 79 ASN cc_start: 0.9090 (m110) cc_final: 0.8624 (p0) REVERT: f 91 LEU cc_start: 0.8815 (mm) cc_final: 0.8389 (pp) REVERT: f 121 GLU cc_start: 0.9259 (pt0) cc_final: 0.8833 (pp20) REVERT: f 124 PHE cc_start: 0.8115 (t80) cc_final: 0.7467 (t80) REVERT: f 548 ASN cc_start: 0.7425 (m110) cc_final: 0.7116 (p0) REVERT: f 610 THR cc_start: 0.9453 (p) cc_final: 0.9206 (p) REVERT: g 79 ASN cc_start: 0.8927 (m-40) cc_final: 0.8501 (p0) REVERT: g 127 TRP cc_start: 0.8590 (t-100) cc_final: 0.8314 (t-100) REVERT: g 548 ASN cc_start: 0.8358 (p0) cc_final: 0.7483 (t0) REVERT: g 600 PHE cc_start: 0.8812 (t80) cc_final: 0.8423 (t80) REVERT: g 608 TYR cc_start: 0.8628 (m-10) cc_final: 0.8301 (m-10) REVERT: h 63 GLU cc_start: 0.8470 (tp30) cc_final: 0.8070 (tp30) REVERT: h 70 GLN cc_start: 0.9191 (mt0) cc_final: 0.8926 (mt0) REVERT: h 79 ASN cc_start: 0.8860 (m110) cc_final: 0.8443 (p0) REVERT: h 229 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7644 (ttp-170) REVERT: h 307 ARG cc_start: 0.8039 (ttt-90) cc_final: 0.7362 (tmm-80) REVERT: h 511 ASN cc_start: 0.9213 (t0) cc_final: 0.8796 (t0) REVERT: h 548 ASN cc_start: 0.7277 (m110) cc_final: 0.6931 (p0) REVERT: i 63 GLU cc_start: 0.8464 (tp30) cc_final: 0.7996 (tp30) REVERT: i 70 GLN cc_start: 0.9244 (mt0) cc_final: 0.9021 (mt0) REVERT: i 160 TYR cc_start: 0.9175 (t80) cc_final: 0.8858 (t80) REVERT: i 304 LEU cc_start: 0.9184 (pp) cc_final: 0.8915 (pp) REVERT: i 307 ARG cc_start: 0.6631 (tpm170) cc_final: 0.6130 (tmm-80) REVERT: i 511 ASN cc_start: 0.9304 (t0) cc_final: 0.8230 (t0) REVERT: i 513 PHE cc_start: 0.8531 (m-80) cc_final: 0.7735 (m-80) REVERT: i 548 ASN cc_start: 0.7697 (m110) cc_final: 0.7269 (p0) REVERT: i 608 TYR cc_start: 0.8797 (m-10) cc_final: 0.7954 (m-10) REVERT: j 29 LYS cc_start: 0.9409 (tmtt) cc_final: 0.9063 (tmtt) REVERT: j 63 GLU cc_start: 0.8179 (tp30) cc_final: 0.7851 (tp30) REVERT: j 70 GLN cc_start: 0.9149 (mt0) cc_final: 0.8814 (mt0) REVERT: j 125 ASP cc_start: 0.9105 (t70) cc_final: 0.8672 (m-30) REVERT: j 200 THR cc_start: 0.8873 (m) cc_final: 0.8576 (p) REVERT: j 304 LEU cc_start: 0.9046 (pp) cc_final: 0.8762 (pp) REVERT: k 214 GLU cc_start: 0.9082 (pp20) cc_final: 0.8863 (pp20) REVERT: k 499 VAL cc_start: 0.9017 (t) cc_final: 0.8769 (p) REVERT: k 535 GLU cc_start: 0.8585 (tp30) cc_final: 0.8118 (tp30) REVERT: l 79 ASN cc_start: 0.8897 (m110) cc_final: 0.8550 (p0) REVERT: l 160 TYR cc_start: 0.9287 (t80) cc_final: 0.8822 (t80) REVERT: l 302 LYS cc_start: 0.9395 (mppt) cc_final: 0.9045 (mppt) REVERT: l 515 HIS cc_start: 0.8337 (t-90) cc_final: 0.8076 (t70) outliers start: 1 outliers final: 0 residues processed: 885 average time/residue: 0.2357 time to fit residues: 327.4314 Evaluate side-chains 685 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 362 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 432 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 405 optimal weight: 0.8980 chunk 458 optimal weight: 7.9990 chunk 210 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 459 optimal weight: 8.9990 chunk 344 optimal weight: 0.0770 chunk 41 optimal weight: 7.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 511 ASN b 549 GLN d 70 GLN ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN g 515 HIS ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 606 GLN ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 551 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083427 restraints weight = 96225.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.085709 restraints weight = 58869.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087103 restraints weight = 43426.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088017 restraints weight = 36179.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088555 restraints weight = 32389.998| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40644 Z= 0.158 Angle : 0.616 10.121 55284 Z= 0.315 Chirality : 0.041 0.152 6048 Planarity : 0.005 0.113 7176 Dihedral : 4.362 23.274 5580 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.37 % 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: 1.45 (0.12), residues: 4920 helix: 2.26 (0.10), residues: 2796 sheet: 0.31 (0.22), residues: 552 loop : -1.25 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG l 530 TYR 0.021 0.001 TYR a 608 PHE 0.035 0.001 PHE j 124 TRP 0.063 0.002 TRP h 127 HIS 0.013 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00359 (40644) covalent geometry : angle 0.61560 (55284) hydrogen bonds : bond 0.03846 ( 2314) hydrogen bonds : angle 4.14711 ( 6732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 863 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 159 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8205 (mtmt) REVERT: a 297 ASN cc_start: 0.8964 (t0) cc_final: 0.8607 (t0) REVERT: a 600 PHE cc_start: 0.8345 (t80) cc_final: 0.8139 (t80) REVERT: b 29 LYS cc_start: 0.9447 (tmtt) cc_final: 0.9185 (tmtt) REVERT: b 70 GLN cc_start: 0.9335 (mt0) cc_final: 0.9026 (mt0) REVERT: b 127 TRP cc_start: 0.8808 (t-100) cc_final: 0.8367 (t-100) REVERT: b 548 ASN cc_start: 0.8373 (p0) cc_final: 0.7617 (m-40) REVERT: b 571 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8215 (mm-30) REVERT: c 70 GLN cc_start: 0.9253 (mt0) cc_final: 0.8842 (mt0) REVERT: c 127 TRP cc_start: 0.8204 (t60) cc_final: 0.7725 (t60) REVERT: c 160 TYR cc_start: 0.9354 (t80) cc_final: 0.8859 (t80) REVERT: c 511 ASN cc_start: 0.8948 (t0) cc_final: 0.8712 (t0) REVERT: c 608 TYR cc_start: 0.8434 (m-10) cc_final: 0.8207 (m-10) REVERT: d 63 GLU cc_start: 0.8552 (tp30) cc_final: 0.8191 (tp30) REVERT: d 79 ASN cc_start: 0.8852 (m-40) cc_final: 0.8448 (p0) REVERT: d 136 LEU cc_start: 0.9372 (tp) cc_final: 0.8646 (tt) REVERT: d 159 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8250 (mtmt) REVERT: d 203 GLU cc_start: 0.8276 (tt0) cc_final: 0.7986 (tt0) REVERT: d 511 ASN cc_start: 0.8876 (t0) cc_final: 0.8524 (t0) REVERT: d 547 ASN cc_start: 0.7230 (t0) cc_final: 0.6834 (p0) REVERT: d 611 ASP cc_start: 0.8533 (m-30) cc_final: 0.8103 (m-30) REVERT: e 79 ASN cc_start: 0.8804 (m-40) cc_final: 0.8549 (p0) REVERT: e 108 TYR cc_start: 0.7243 (m-80) cc_final: 0.6448 (p90) REVERT: e 511 ASN cc_start: 0.8695 (t0) cc_final: 0.8426 (t0) REVERT: e 548 ASN cc_start: 0.8564 (p0) cc_final: 0.8017 (m110) REVERT: f 79 ASN cc_start: 0.8979 (m110) cc_final: 0.8651 (p0) REVERT: f 91 LEU cc_start: 0.8977 (mm) cc_final: 0.8483 (pp) REVERT: f 121 GLU cc_start: 0.9239 (pt0) cc_final: 0.8815 (pp20) REVERT: f 124 PHE cc_start: 0.8046 (t80) cc_final: 0.7525 (t80) REVERT: f 548 ASN cc_start: 0.7441 (m110) cc_final: 0.7144 (p0) REVERT: g 79 ASN cc_start: 0.8924 (m-40) cc_final: 0.8505 (p0) REVERT: g 127 TRP cc_start: 0.8593 (t-100) cc_final: 0.8290 (t-100) REVERT: g 304 LEU cc_start: 0.8985 (pp) cc_final: 0.8718 (pp) REVERT: g 548 ASN cc_start: 0.8375 (p0) cc_final: 0.7469 (t0) REVERT: g 600 PHE cc_start: 0.8644 (t80) cc_final: 0.8075 (t80) REVERT: g 608 TYR cc_start: 0.8584 (m-10) cc_final: 0.8316 (m-10) REVERT: h 63 GLU cc_start: 0.8529 (tp30) cc_final: 0.8096 (tp30) REVERT: h 79 ASN cc_start: 0.8874 (m110) cc_final: 0.8461 (p0) REVERT: h 307 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.7441 (tmm-80) REVERT: h 511 ASN cc_start: 0.9161 (t0) cc_final: 0.8888 (t0) REVERT: h 548 ASN cc_start: 0.7390 (m110) cc_final: 0.7041 (p0) REVERT: i 63 GLU cc_start: 0.8442 (tp30) cc_final: 0.7960 (tp30) REVERT: i 70 GLN cc_start: 0.9245 (mt0) cc_final: 0.9013 (mt0) REVERT: i 160 TYR cc_start: 0.9177 (t80) cc_final: 0.8874 (t80) REVERT: i 307 ARG cc_start: 0.6745 (tpm170) cc_final: 0.6186 (tmm-80) REVERT: i 511 ASN cc_start: 0.9304 (t0) cc_final: 0.8229 (t0) REVERT: i 513 PHE cc_start: 0.8557 (m-80) cc_final: 0.7717 (m-80) REVERT: i 548 ASN cc_start: 0.7718 (m110) cc_final: 0.7259 (p0) REVERT: i 608 TYR cc_start: 0.8757 (m-10) cc_final: 0.7881 (m-10) REVERT: j 63 GLU cc_start: 0.8204 (tp30) cc_final: 0.7868 (tp30) REVERT: j 70 GLN cc_start: 0.9159 (mt0) cc_final: 0.8798 (mt0) REVERT: j 125 ASP cc_start: 0.8952 (t70) cc_final: 0.8555 (m-30) REVERT: j 127 TRP cc_start: 0.8342 (t-100) cc_final: 0.8076 (t-100) REVERT: j 200 THR cc_start: 0.8895 (m) cc_final: 0.8588 (p) REVERT: j 231 TYR cc_start: 0.7733 (m-80) cc_final: 0.7353 (m-80) REVERT: j 304 LEU cc_start: 0.9079 (pp) cc_final: 0.8810 (pp) REVERT: k 124 PHE cc_start: 0.7674 (t80) cc_final: 0.7174 (t80) REVERT: k 214 GLU cc_start: 0.9073 (pp20) cc_final: 0.8834 (pp20) REVERT: k 499 VAL cc_start: 0.9065 (t) cc_final: 0.8793 (p) REVERT: k 535 GLU cc_start: 0.8597 (tp30) cc_final: 0.8161 (tp30) REVERT: l 79 ASN cc_start: 0.8895 (m110) cc_final: 0.8545 (p0) REVERT: l 124 PHE cc_start: 0.7131 (t80) cc_final: 0.6892 (t80) REVERT: l 160 TYR cc_start: 0.9265 (t80) cc_final: 0.8816 (t80) REVERT: l 302 LYS cc_start: 0.9381 (mppt) cc_final: 0.9045 (mppt) REVERT: l 515 HIS cc_start: 0.8307 (t-90) cc_final: 0.8057 (t70) REVERT: l 574 LEU cc_start: 0.9302 (tp) cc_final: 0.9070 (tp) outliers start: 3 outliers final: 0 residues processed: 863 average time/residue: 0.2346 time to fit residues: 319.9259 Evaluate side-chains 667 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 337 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 201 optimal weight: 0.0270 chunk 261 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 326 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 511 ASN b 549 GLN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN g 515 HIS ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 ASN ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 129 ASN ** l 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 551 GLN ** l 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085016 restraints weight = 96045.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087336 restraints weight = 58430.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088745 restraints weight = 42883.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089675 restraints weight = 35665.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090139 restraints weight = 31921.469| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 40644 Z= 0.123 Angle : 0.601 8.474 55284 Z= 0.305 Chirality : 0.041 0.159 6048 Planarity : 0.005 0.116 7176 Dihedral : 4.287 21.628 5580 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.10 % Allowed : 1.91 % Favored : 98.00 % 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: 1.49 (0.12), residues: 4920 helix: 2.27 (0.10), residues: 2796 sheet: 0.42 (0.22), residues: 552 loop : -1.22 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG e 122 TYR 0.030 0.001 TYR c 108 PHE 0.030 0.001 PHE a 124 TRP 0.075 0.002 TRP h 127 HIS 0.011 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00275 (40644) covalent geometry : angle 0.60138 (55284) hydrogen bonds : bond 0.03643 ( 2314) hydrogen bonds : angle 4.02766 ( 6732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 886 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 129 ASN cc_start: 0.9074 (t0) cc_final: 0.8687 (t0) REVERT: a 600 PHE cc_start: 0.8351 (t80) cc_final: 0.8011 (t80) REVERT: b 29 LYS cc_start: 0.9409 (tmtt) cc_final: 0.9199 (tmtt) REVERT: b 70 GLN cc_start: 0.9313 (mt0) cc_final: 0.8969 (mt0) REVERT: b 127 TRP cc_start: 0.8760 (t-100) cc_final: 0.8339 (t-100) REVERT: b 548 ASN cc_start: 0.8350 (p0) cc_final: 0.7576 (m-40) REVERT: b 601 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8375 (mmtm) REVERT: c 70 GLN cc_start: 0.9184 (mt0) cc_final: 0.8856 (mt0) REVERT: c 127 TRP cc_start: 0.8166 (t60) cc_final: 0.7668 (t60) REVERT: c 160 TYR cc_start: 0.9326 (t80) cc_final: 0.8784 (t80) REVERT: c 511 ASN cc_start: 0.8901 (t0) cc_final: 0.8693 (t0) REVERT: c 608 TYR cc_start: 0.8379 (m-10) cc_final: 0.8175 (m-10) REVERT: d 63 GLU cc_start: 0.8330 (tp30) cc_final: 0.8094 (tp30) REVERT: d 79 ASN cc_start: 0.8869 (m-40) cc_final: 0.8491 (p0) REVERT: d 128 ARG cc_start: 0.9373 (pmt-80) cc_final: 0.9151 (pmt-80) REVERT: d 136 LEU cc_start: 0.9347 (tp) cc_final: 0.8614 (tt) REVERT: d 159 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8308 (mtmt) REVERT: d 203 GLU cc_start: 0.8240 (tt0) cc_final: 0.7884 (tt0) REVERT: d 511 ASN cc_start: 0.8861 (t0) cc_final: 0.8604 (t0) REVERT: d 547 ASN cc_start: 0.7235 (t0) cc_final: 0.6857 (p0) REVERT: d 608 TYR cc_start: 0.8619 (m-10) cc_final: 0.8065 (m-10) REVERT: d 611 ASP cc_start: 0.8305 (m-30) cc_final: 0.7989 (m-30) REVERT: e 79 ASN cc_start: 0.8740 (m-40) cc_final: 0.8501 (p0) REVERT: e 108 TYR cc_start: 0.7400 (m-80) cc_final: 0.6687 (p90) REVERT: e 214 GLU cc_start: 0.8996 (pp20) cc_final: 0.8735 (pp20) REVERT: e 511 ASN cc_start: 0.8672 (t0) cc_final: 0.8358 (t0) REVERT: e 548 ASN cc_start: 0.8559 (p0) cc_final: 0.8002 (m110) REVERT: f 79 ASN cc_start: 0.8941 (m110) cc_final: 0.8635 (p0) REVERT: f 121 GLU cc_start: 0.9253 (pt0) cc_final: 0.8820 (pp20) REVERT: f 124 PHE cc_start: 0.7935 (t80) cc_final: 0.7476 (t80) REVERT: f 548 ASN cc_start: 0.7463 (m110) cc_final: 0.7188 (p0) REVERT: g 79 ASN cc_start: 0.8876 (m-40) cc_final: 0.8474 (p0) REVERT: g 122 ARG cc_start: 0.9221 (ttp-170) cc_final: 0.9010 (ptm160) REVERT: g 127 TRP cc_start: 0.8587 (t-100) cc_final: 0.8282 (t-100) REVERT: g 304 LEU cc_start: 0.8892 (pp) cc_final: 0.8625 (pp) REVERT: g 548 ASN cc_start: 0.8406 (p0) cc_final: 0.7498 (t0) REVERT: g 600 PHE cc_start: 0.8595 (t80) cc_final: 0.8143 (t80) REVERT: g 608 TYR cc_start: 0.8554 (m-10) cc_final: 0.8265 (m-10) REVERT: h 63 GLU cc_start: 0.8457 (tp30) cc_final: 0.8037 (tp30) REVERT: h 79 ASN cc_start: 0.8868 (m110) cc_final: 0.8499 (p0) REVERT: h 229 ARG cc_start: 0.8287 (ttp-110) cc_final: 0.8058 (ttp-170) REVERT: h 307 ARG cc_start: 0.8026 (ttt-90) cc_final: 0.7493 (tmm-80) REVERT: h 511 ASN cc_start: 0.9015 (t0) cc_final: 0.8775 (t0) REVERT: h 548 ASN cc_start: 0.7644 (m110) cc_final: 0.7235 (p0) REVERT: i 63 GLU cc_start: 0.8414 (tp30) cc_final: 0.7935 (tp30) REVERT: i 110 ASN cc_start: 0.3464 (OUTLIER) cc_final: 0.2297 (t0) REVERT: i 160 TYR cc_start: 0.9104 (t80) cc_final: 0.8795 (t80) REVERT: i 307 ARG cc_start: 0.6869 (tpm170) cc_final: 0.6284 (tmm-80) REVERT: i 511 ASN cc_start: 0.9223 (t0) cc_final: 0.8203 (t0) REVERT: i 513 PHE cc_start: 0.8481 (m-80) cc_final: 0.7653 (m-80) REVERT: i 548 ASN cc_start: 0.7716 (m110) cc_final: 0.7277 (p0) REVERT: i 608 TYR cc_start: 0.8728 (m-10) cc_final: 0.7809 (m-10) REVERT: j 63 GLU cc_start: 0.8139 (tp30) cc_final: 0.7834 (tp30) REVERT: j 70 GLN cc_start: 0.9140 (mt0) cc_final: 0.8783 (mt0) REVERT: j 125 ASP cc_start: 0.8935 (t70) cc_final: 0.8543 (m-30) REVERT: j 127 TRP cc_start: 0.8443 (t-100) cc_final: 0.8138 (t-100) REVERT: j 159 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8763 (mtmt) REVERT: j 200 THR cc_start: 0.8895 (m) cc_final: 0.8616 (p) REVERT: j 304 LEU cc_start: 0.8990 (pp) cc_final: 0.8749 (pp) REVERT: k 132 ARG cc_start: 0.9280 (mtp85) cc_final: 0.8875 (mtp85) REVERT: k 214 GLU cc_start: 0.9056 (pp20) cc_final: 0.8794 (pp20) REVERT: k 499 VAL cc_start: 0.8989 (t) cc_final: 0.8743 (p) REVERT: k 515 HIS cc_start: 0.8286 (t70) cc_final: 0.8044 (t-170) REVERT: k 535 GLU cc_start: 0.8527 (tp30) cc_final: 0.8083 (tp30) REVERT: l 70 GLN cc_start: 0.9064 (mt0) cc_final: 0.8640 (mt0) REVERT: l 79 ASN cc_start: 0.8800 (m110) cc_final: 0.8510 (p0) REVERT: l 121 GLU cc_start: 0.8898 (tt0) cc_final: 0.8617 (tm-30) REVERT: l 122 ARG cc_start: 0.8907 (ptt180) cc_final: 0.8597 (ptm160) REVERT: l 160 TYR cc_start: 0.9204 (t80) cc_final: 0.8740 (t80) REVERT: l 302 LYS cc_start: 0.9369 (mppt) cc_final: 0.9011 (mppt) REVERT: l 571 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8333 (mm-30) REVERT: l 578 ARG cc_start: 0.7232 (mmp80) cc_final: 0.6864 (mmp80) outliers start: 4 outliers final: 0 residues processed: 887 average time/residue: 0.2428 time to fit residues: 339.4637 Evaluate side-chains 670 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 669 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 433 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 chunk 481 optimal weight: 7.9990 chunk 352 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 324 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 206 optimal weight: 0.3980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 511 ASN b 549 GLN ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN g 515 HIS ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 ASN ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 297 ASN ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 551 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.121822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085126 restraints weight = 96245.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087435 restraints weight = 58983.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088893 restraints weight = 43508.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089771 restraints weight = 36144.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090243 restraints weight = 32430.426| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40644 Z= 0.127 Angle : 0.620 10.679 55284 Z= 0.313 Chirality : 0.041 0.156 6048 Planarity : 0.004 0.060 7176 Dihedral : 4.283 21.135 5580 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 1.47 % Favored : 98.43 % 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: 1.45 (0.12), residues: 4920 helix: 2.24 (0.10), residues: 2796 sheet: 0.31 (0.21), residues: 600 loop : -1.26 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG e 122 TYR 0.025 0.001 TYR c 108 PHE 0.032 0.001 PHE l 616 TRP 0.055 0.002 TRP i 262 HIS 0.011 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00286 (40644) covalent geometry : angle 0.61998 (55284) hydrogen bonds : bond 0.03638 ( 2314) hydrogen bonds : angle 4.01805 ( 6732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 849 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 128 ARG cc_start: 0.9161 (pmt-80) cc_final: 0.8900 (pmt-80) REVERT: a 600 PHE cc_start: 0.8300 (t80) cc_final: 0.7942 (t80) REVERT: b 70 GLN cc_start: 0.9324 (mt0) cc_final: 0.9018 (mt0) REVERT: b 127 TRP cc_start: 0.8769 (t-100) cc_final: 0.8391 (t-100) REVERT: b 548 ASN cc_start: 0.8388 (p0) cc_final: 0.7519 (m-40) REVERT: b 601 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8415 (mmtm) REVERT: c 70 GLN cc_start: 0.9218 (mt0) cc_final: 0.8835 (mt0) REVERT: c 127 TRP cc_start: 0.8149 (t60) cc_final: 0.7618 (t60) REVERT: c 160 TYR cc_start: 0.9325 (t80) cc_final: 0.8814 (t80) REVERT: c 526 GLU cc_start: 0.8409 (tp30) cc_final: 0.7964 (tp30) REVERT: d 63 GLU cc_start: 0.8421 (tp30) cc_final: 0.8043 (tp30) REVERT: d 79 ASN cc_start: 0.8847 (m-40) cc_final: 0.8463 (p0) REVERT: d 136 LEU cc_start: 0.9359 (tp) cc_final: 0.8937 (tp) REVERT: d 159 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8298 (mtmt) REVERT: d 203 GLU cc_start: 0.8281 (tt0) cc_final: 0.8008 (tt0) REVERT: d 511 ASN cc_start: 0.8863 (t0) cc_final: 0.8516 (t0) REVERT: d 547 ASN cc_start: 0.7220 (t0) cc_final: 0.6850 (p0) REVERT: d 574 LEU cc_start: 0.9390 (tp) cc_final: 0.9106 (tp) REVERT: d 608 TYR cc_start: 0.8621 (m-10) cc_final: 0.8083 (m-10) REVERT: d 611 ASP cc_start: 0.8262 (m-30) cc_final: 0.8053 (m-30) REVERT: e 79 ASN cc_start: 0.8742 (m-40) cc_final: 0.8484 (p0) REVERT: e 108 TYR cc_start: 0.7155 (m-80) cc_final: 0.6621 (p90) REVERT: e 214 GLU cc_start: 0.9043 (pp20) cc_final: 0.8774 (pp20) REVERT: e 511 ASN cc_start: 0.8686 (t0) cc_final: 0.8373 (t0) REVERT: e 548 ASN cc_start: 0.8582 (p0) cc_final: 0.8011 (m110) REVERT: f 124 PHE cc_start: 0.8110 (t80) cc_final: 0.7612 (t80) REVERT: f 127 TRP cc_start: 0.8693 (t-100) cc_final: 0.8221 (t-100) REVERT: f 128 ARG cc_start: 0.9344 (pmt-80) cc_final: 0.9058 (pmt-80) REVERT: f 548 ASN cc_start: 0.7478 (m110) cc_final: 0.7199 (p0) REVERT: g 79 ASN cc_start: 0.8873 (m-40) cc_final: 0.8440 (p0) REVERT: g 127 TRP cc_start: 0.8564 (t-100) cc_final: 0.8291 (t-100) REVERT: g 304 LEU cc_start: 0.8922 (pp) cc_final: 0.8655 (pp) REVERT: g 548 ASN cc_start: 0.8382 (p0) cc_final: 0.7415 (t0) REVERT: g 600 PHE cc_start: 0.8506 (t80) cc_final: 0.8026 (t80) REVERT: g 608 TYR cc_start: 0.8549 (m-10) cc_final: 0.8310 (m-10) REVERT: h 63 GLU cc_start: 0.8532 (tp30) cc_final: 0.8089 (tp30) REVERT: h 79 ASN cc_start: 0.8824 (m110) cc_final: 0.8413 (p0) REVERT: h 307 ARG cc_start: 0.8041 (ttt-90) cc_final: 0.7343 (tmm-80) REVERT: h 511 ASN cc_start: 0.9020 (t0) cc_final: 0.8667 (t0) REVERT: h 548 ASN cc_start: 0.7659 (m110) cc_final: 0.7258 (p0) REVERT: i 63 GLU cc_start: 0.8363 (tp30) cc_final: 0.7939 (tp30) REVERT: i 70 GLN cc_start: 0.9236 (mt0) cc_final: 0.8974 (mt0) REVERT: i 160 TYR cc_start: 0.9088 (t80) cc_final: 0.8788 (t80) REVERT: i 307 ARG cc_start: 0.6890 (tpm170) cc_final: 0.6234 (tmm-80) REVERT: i 511 ASN cc_start: 0.9228 (t0) cc_final: 0.8151 (t0) REVERT: i 513 PHE cc_start: 0.8477 (m-80) cc_final: 0.7650 (m-80) REVERT: i 548 ASN cc_start: 0.7796 (m110) cc_final: 0.7314 (p0) REVERT: i 608 TYR cc_start: 0.8720 (m-10) cc_final: 0.7830 (m-10) REVERT: j 63 GLU cc_start: 0.8162 (tp30) cc_final: 0.7822 (tp30) REVERT: j 70 GLN cc_start: 0.9177 (mt0) cc_final: 0.8817 (mt0) REVERT: j 125 ASP cc_start: 0.8953 (t70) cc_final: 0.8580 (m-30) REVERT: j 127 TRP cc_start: 0.8443 (t-100) cc_final: 0.8133 (t-100) REVERT: j 231 TYR cc_start: 0.7723 (m-80) cc_final: 0.7309 (m-80) REVERT: j 304 LEU cc_start: 0.8998 (pp) cc_final: 0.8773 (pp) REVERT: k 128 ARG cc_start: 0.9480 (pmt-80) cc_final: 0.9209 (pmt-80) REVERT: k 132 ARG cc_start: 0.9209 (mtp85) cc_final: 0.8946 (mtp85) REVERT: k 214 GLU cc_start: 0.9025 (pp20) cc_final: 0.8776 (pp20) REVERT: k 499 VAL cc_start: 0.9013 (t) cc_final: 0.8757 (p) REVERT: k 535 GLU cc_start: 0.8523 (tp30) cc_final: 0.8034 (tp30) REVERT: l 70 GLN cc_start: 0.9067 (mt0) cc_final: 0.8659 (mt0) REVERT: l 79 ASN cc_start: 0.8783 (m110) cc_final: 0.8514 (p0) REVERT: l 121 GLU cc_start: 0.8960 (tt0) cc_final: 0.8657 (tm-30) REVERT: l 122 ARG cc_start: 0.8789 (ptt180) cc_final: 0.8581 (ptm160) REVERT: l 128 ARG cc_start: 0.9216 (pmt-80) cc_final: 0.8895 (pmt-80) REVERT: l 160 TYR cc_start: 0.9230 (t80) cc_final: 0.8787 (t80) REVERT: l 302 LYS cc_start: 0.9385 (mppt) cc_final: 0.8882 (mptt) REVERT: l 571 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8323 (mm-30) REVERT: l 578 ARG cc_start: 0.7177 (mmp80) cc_final: 0.6884 (mmp80) outliers start: 4 outliers final: 0 residues processed: 850 average time/residue: 0.2344 time to fit residues: 313.2882 Evaluate side-chains 652 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 138 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 436 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 449 optimal weight: 0.0370 chunk 396 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 317 optimal weight: 3.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 515 HIS ** b 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 511 ASN c 297 ASN d 70 GLN ** d 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 44 HIS ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 HIS ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.085647 restraints weight = 95206.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087971 restraints weight = 58011.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.089453 restraints weight = 42580.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.090354 restraints weight = 35276.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.090803 restraints weight = 31575.083| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40644 Z= 0.125 Angle : 0.624 8.435 55284 Z= 0.314 Chirality : 0.041 0.233 6048 Planarity : 0.004 0.056 7176 Dihedral : 4.278 20.939 5580 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.96 % 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: 1.41 (0.12), residues: 4920 helix: 2.18 (0.10), residues: 2796 sheet: 0.36 (0.21), residues: 600 loop : -1.25 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 296 TYR 0.025 0.001 TYR c 108 PHE 0.033 0.002 PHE a 616 TRP 0.082 0.002 TRP e 127 HIS 0.010 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00276 (40644) covalent geometry : angle 0.62397 (55284) hydrogen bonds : bond 0.03630 ( 2314) hydrogen bonds : angle 4.00448 ( 6732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 850 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 129 ASN cc_start: 0.9305 (t0) cc_final: 0.8989 (t0) REVERT: a 600 PHE cc_start: 0.8343 (t80) cc_final: 0.7921 (t80) REVERT: b 29 LYS cc_start: 0.9349 (tmtt) cc_final: 0.8985 (tmtt) REVERT: b 70 GLN cc_start: 0.9324 (mt0) cc_final: 0.8926 (mt0) REVERT: b 548 ASN cc_start: 0.8301 (p0) cc_final: 0.7399 (m-40) REVERT: c 70 GLN cc_start: 0.9287 (mt0) cc_final: 0.8897 (mt0) REVERT: c 127 TRP cc_start: 0.8106 (t60) cc_final: 0.7636 (t60) REVERT: d 63 GLU cc_start: 0.8512 (tp30) cc_final: 0.8133 (tp30) REVERT: d 79 ASN cc_start: 0.8807 (m-40) cc_final: 0.8429 (p0) REVERT: d 128 ARG cc_start: 0.9377 (pmt-80) cc_final: 0.9080 (pmt-80) REVERT: d 159 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8279 (mtmt) REVERT: d 203 GLU cc_start: 0.8255 (tt0) cc_final: 0.7997 (tt0) REVERT: d 226 ASP cc_start: 0.8165 (m-30) cc_final: 0.7944 (m-30) REVERT: d 511 ASN cc_start: 0.8837 (t0) cc_final: 0.8594 (t0) REVERT: d 547 ASN cc_start: 0.7178 (t0) cc_final: 0.6824 (p0) REVERT: d 574 LEU cc_start: 0.9362 (tp) cc_final: 0.9077 (tp) REVERT: d 608 TYR cc_start: 0.8564 (m-10) cc_final: 0.8136 (m-10) REVERT: d 611 ASP cc_start: 0.8506 (m-30) cc_final: 0.8035 (m-30) REVERT: e 79 ASN cc_start: 0.8700 (m-40) cc_final: 0.8469 (p0) REVERT: e 214 GLU cc_start: 0.9042 (pp20) cc_final: 0.8782 (pp20) REVERT: e 511 ASN cc_start: 0.8656 (t0) cc_final: 0.8340 (t0) REVERT: e 548 ASN cc_start: 0.8550 (p0) cc_final: 0.7983 (m110) REVERT: f 100 GLN cc_start: 0.8142 (mt0) cc_final: 0.7803 (mp10) REVERT: f 124 PHE cc_start: 0.7939 (t80) cc_final: 0.7521 (t80) REVERT: f 548 ASN cc_start: 0.7484 (m110) cc_final: 0.7176 (p0) REVERT: g 79 ASN cc_start: 0.8849 (m-40) cc_final: 0.8428 (p0) REVERT: g 127 TRP cc_start: 0.8493 (t-100) cc_final: 0.8222 (t-100) REVERT: g 297 ASN cc_start: 0.8962 (t0) cc_final: 0.8750 (t0) REVERT: g 304 LEU cc_start: 0.8885 (pp) cc_final: 0.8650 (pp) REVERT: g 548 ASN cc_start: 0.8457 (p0) cc_final: 0.7502 (t0) REVERT: g 600 PHE cc_start: 0.8437 (t80) cc_final: 0.7951 (t80) REVERT: g 608 TYR cc_start: 0.8495 (m-10) cc_final: 0.8259 (m-10) REVERT: h 63 GLU cc_start: 0.8549 (tp30) cc_final: 0.8074 (tp30) REVERT: h 79 ASN cc_start: 0.8775 (m110) cc_final: 0.8407 (p0) REVERT: h 307 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7363 (tmm-80) REVERT: h 511 ASN cc_start: 0.8997 (t0) cc_final: 0.8666 (t0) REVERT: h 548 ASN cc_start: 0.7669 (m110) cc_final: 0.7269 (p0) REVERT: i 63 GLU cc_start: 0.8387 (tp30) cc_final: 0.8094 (tp30) REVERT: i 160 TYR cc_start: 0.9079 (t80) cc_final: 0.8781 (t80) REVERT: i 307 ARG cc_start: 0.6959 (tpm170) cc_final: 0.6283 (tmm-80) REVERT: i 511 ASN cc_start: 0.9210 (t0) cc_final: 0.8126 (t0) REVERT: i 513 PHE cc_start: 0.8484 (m-80) cc_final: 0.7640 (m-80) REVERT: i 548 ASN cc_start: 0.7804 (m110) cc_final: 0.7324 (p0) REVERT: i 608 TYR cc_start: 0.8691 (m-10) cc_final: 0.7825 (m-10) REVERT: j 29 LYS cc_start: 0.9398 (tmtt) cc_final: 0.8828 (tmtt) REVERT: j 63 GLU cc_start: 0.8138 (tp30) cc_final: 0.7795 (tp30) REVERT: j 70 GLN cc_start: 0.9106 (mt0) cc_final: 0.8768 (mt0) REVERT: j 125 ASP cc_start: 0.8876 (t70) cc_final: 0.8475 (m-30) REVERT: j 127 TRP cc_start: 0.8477 (t-100) cc_final: 0.8178 (t-100) REVERT: j 304 LEU cc_start: 0.8976 (pp) cc_final: 0.8737 (pp) REVERT: k 132 ARG cc_start: 0.9142 (mtp85) cc_final: 0.8877 (mtp85) REVERT: k 214 GLU cc_start: 0.9019 (pp20) cc_final: 0.8784 (pp20) REVERT: k 499 VAL cc_start: 0.8994 (t) cc_final: 0.8752 (p) REVERT: k 535 GLU cc_start: 0.8515 (tp30) cc_final: 0.8077 (tp30) REVERT: l 79 ASN cc_start: 0.8719 (m110) cc_final: 0.8497 (p0) REVERT: l 121 GLU cc_start: 0.8942 (tt0) cc_final: 0.8666 (tm-30) REVERT: l 122 ARG cc_start: 0.8836 (ptt180) cc_final: 0.8585 (ptm160) REVERT: l 160 TYR cc_start: 0.9248 (t80) cc_final: 0.8806 (t80) REVERT: l 302 LYS cc_start: 0.9357 (mppt) cc_final: 0.8847 (mptt) outliers start: 4 outliers final: 0 residues processed: 850 average time/residue: 0.2217 time to fit residues: 301.3177 Evaluate side-chains 639 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 336 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 360 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 44 HIS ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 511 ASN b 549 GLN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 110 ASN ** d 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 HIS k 545 HIS ** l 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083525 restraints weight = 96654.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085784 restraints weight = 59443.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087137 restraints weight = 43930.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088022 restraints weight = 36760.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.088551 restraints weight = 33041.054| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 40644 Z= 0.164 Angle : 0.653 13.047 55284 Z= 0.332 Chirality : 0.042 0.183 6048 Planarity : 0.005 0.050 7176 Dihedral : 4.354 22.539 5580 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.10 % Allowed : 0.87 % Favored : 99.03 % 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: 1.32 (0.12), residues: 4920 helix: 2.12 (0.10), residues: 2796 sheet: 0.28 (0.21), residues: 600 loop : -1.29 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 296 TYR 0.045 0.002 TYR a 608 PHE 0.034 0.002 PHE c 74 TRP 0.093 0.003 TRP e 127 HIS 0.012 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00380 (40644) covalent geometry : angle 0.65317 (55284) hydrogen bonds : bond 0.03872 ( 2314) hydrogen bonds : angle 4.14519 ( 6732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 828 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 128 ARG cc_start: 0.9263 (pmt-80) cc_final: 0.8877 (pmt-80) REVERT: a 129 ASN cc_start: 0.9322 (t0) cc_final: 0.8937 (t0) REVERT: a 279 GLU cc_start: 0.8044 (mp0) cc_final: 0.7843 (mp0) REVERT: a 600 PHE cc_start: 0.8416 (t80) cc_final: 0.7954 (t80) REVERT: b 29 LYS cc_start: 0.9476 (tmtt) cc_final: 0.8980 (tmtt) REVERT: b 70 GLN cc_start: 0.9338 (mt0) cc_final: 0.9012 (mt0) REVERT: b 548 ASN cc_start: 0.8335 (p0) cc_final: 0.7401 (m-40) REVERT: c 70 GLN cc_start: 0.9239 (mt0) cc_final: 0.8898 (mt0) REVERT: c 127 TRP cc_start: 0.8171 (t60) cc_final: 0.7692 (t60) REVERT: d 63 GLU cc_start: 0.8472 (tp30) cc_final: 0.8136 (tp30) REVERT: d 79 ASN cc_start: 0.8842 (m-40) cc_final: 0.8449 (p0) REVERT: d 127 TRP cc_start: 0.8442 (t-100) cc_final: 0.8082 (t-100) REVERT: d 128 ARG cc_start: 0.9457 (pmt-80) cc_final: 0.9117 (pmt-80) REVERT: d 159 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8252 (mtmt) REVERT: d 203 GLU cc_start: 0.8283 (tt0) cc_final: 0.8006 (tt0) REVERT: d 226 ASP cc_start: 0.8130 (m-30) cc_final: 0.7920 (m-30) REVERT: d 511 ASN cc_start: 0.8891 (t0) cc_final: 0.8523 (t0) REVERT: d 547 ASN cc_start: 0.7095 (t0) cc_final: 0.6709 (p0) REVERT: d 574 LEU cc_start: 0.9403 (tp) cc_final: 0.9086 (tp) REVERT: d 608 TYR cc_start: 0.8635 (m-10) cc_final: 0.8151 (m-10) REVERT: d 611 ASP cc_start: 0.8594 (m-30) cc_final: 0.8131 (m-30) REVERT: e 79 ASN cc_start: 0.8772 (m-40) cc_final: 0.8497 (p0) REVERT: e 108 TYR cc_start: 0.7279 (m-80) cc_final: 0.6497 (p90) REVERT: e 125 ASP cc_start: 0.8626 (t0) cc_final: 0.8372 (m-30) REVERT: e 214 GLU cc_start: 0.9101 (pp20) cc_final: 0.8831 (pp20) REVERT: e 511 ASN cc_start: 0.8721 (t0) cc_final: 0.8334 (t0) REVERT: e 548 ASN cc_start: 0.8571 (p0) cc_final: 0.8058 (m-40) REVERT: f 79 ASN cc_start: 0.8958 (m110) cc_final: 0.8646 (p0) REVERT: f 100 GLN cc_start: 0.8224 (mt0) cc_final: 0.7867 (mp10) REVERT: f 124 PHE cc_start: 0.8087 (t80) cc_final: 0.7610 (t80) REVERT: f 548 ASN cc_start: 0.7485 (m110) cc_final: 0.7198 (p0) REVERT: g 79 ASN cc_start: 0.8909 (m-40) cc_final: 0.8452 (p0) REVERT: g 127 TRP cc_start: 0.8539 (t-100) cc_final: 0.8319 (t-100) REVERT: g 213 PHE cc_start: 0.8988 (m-10) cc_final: 0.8737 (m-80) REVERT: g 297 ASN cc_start: 0.8969 (t0) cc_final: 0.8712 (t0) REVERT: g 304 LEU cc_start: 0.9013 (pp) cc_final: 0.8735 (pp) REVERT: g 600 PHE cc_start: 0.8446 (t80) cc_final: 0.7938 (t80) REVERT: h 63 GLU cc_start: 0.8621 (tp30) cc_final: 0.8151 (tp30) REVERT: h 79 ASN cc_start: 0.8823 (m110) cc_final: 0.8430 (p0) REVERT: h 307 ARG cc_start: 0.8083 (ttt-90) cc_final: 0.7583 (tmm-80) REVERT: h 511 ASN cc_start: 0.9070 (t0) cc_final: 0.8705 (t0) REVERT: h 548 ASN cc_start: 0.7473 (m110) cc_final: 0.7149 (p0) REVERT: i 63 GLU cc_start: 0.8448 (tp30) cc_final: 0.8174 (tp30) REVERT: i 160 TYR cc_start: 0.9121 (t80) cc_final: 0.8847 (t80) REVERT: i 307 ARG cc_start: 0.7019 (tpm170) cc_final: 0.6324 (tmm-80) REVERT: i 511 ASN cc_start: 0.9312 (t0) cc_final: 0.8684 (t0) REVERT: i 513 PHE cc_start: 0.8523 (m-80) cc_final: 0.7883 (m-80) REVERT: i 548 ASN cc_start: 0.7832 (m110) cc_final: 0.7342 (p0) REVERT: i 608 TYR cc_start: 0.8683 (m-10) cc_final: 0.7753 (m-10) REVERT: j 29 LYS cc_start: 0.9376 (tmtt) cc_final: 0.8916 (tmtt) REVERT: j 63 GLU cc_start: 0.8228 (tp30) cc_final: 0.7863 (tp30) REVERT: j 70 GLN cc_start: 0.9162 (mt0) cc_final: 0.8844 (mt0) REVERT: j 125 ASP cc_start: 0.8823 (t70) cc_final: 0.8529 (m-30) REVERT: j 127 TRP cc_start: 0.8525 (t-100) cc_final: 0.8203 (t-100) REVERT: j 129 ASN cc_start: 0.9056 (t0) cc_final: 0.8792 (p0) REVERT: j 304 LEU cc_start: 0.9121 (pp) cc_final: 0.8868 (pp) REVERT: k 128 ARG cc_start: 0.9496 (pmt-80) cc_final: 0.9040 (pmt-80) REVERT: k 214 GLU cc_start: 0.9015 (pp20) cc_final: 0.8772 (pp20) REVERT: k 499 VAL cc_start: 0.9062 (t) cc_final: 0.8784 (p) REVERT: k 535 GLU cc_start: 0.8566 (tp30) cc_final: 0.8214 (tp30) REVERT: l 79 ASN cc_start: 0.8794 (m110) cc_final: 0.8522 (p0) REVERT: l 121 GLU cc_start: 0.8954 (tt0) cc_final: 0.8634 (tm-30) REVERT: l 128 ARG cc_start: 0.9231 (pmt-80) cc_final: 0.8859 (pmt-80) REVERT: l 160 TYR cc_start: 0.9314 (t80) cc_final: 0.8879 (t80) REVERT: l 302 LYS cc_start: 0.9373 (mppt) cc_final: 0.8937 (mptt) outliers start: 4 outliers final: 0 residues processed: 829 average time/residue: 0.2371 time to fit residues: 312.4716 Evaluate side-chains 625 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 167 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 404 optimal weight: 0.9980 chunk 360 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 470 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 49 optimal weight: 0.0470 chunk 370 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 44 HIS a 57 ASN ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 511 ASN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN g 534 HIS ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 HIS ** l 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.122009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.085433 restraints weight = 95436.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087693 restraints weight = 58779.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.089118 restraints weight = 43496.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089974 restraints weight = 36310.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090419 restraints weight = 32661.755| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40644 Z= 0.126 Angle : 0.649 11.456 55284 Z= 0.324 Chirality : 0.042 0.182 6048 Planarity : 0.005 0.072 7176 Dihedral : 4.308 23.034 5580 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % 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: 1.33 (0.12), residues: 4920 helix: 2.10 (0.10), residues: 2796 sheet: 0.35 (0.21), residues: 600 loop : -1.26 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG b 530 TYR 0.037 0.001 TYR a 608 PHE 0.037 0.001 PHE c 74 TRP 0.053 0.002 TRP e 127 HIS 0.010 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00279 (40644) covalent geometry : angle 0.64908 (55284) hydrogen bonds : bond 0.03655 ( 2314) hydrogen bonds : angle 4.06573 ( 6732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 836 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 128 ARG cc_start: 0.9205 (pmt-80) cc_final: 0.8823 (pmt-80) REVERT: a 129 ASN cc_start: 0.9313 (t0) cc_final: 0.8843 (t0) REVERT: a 279 GLU cc_start: 0.7974 (mp0) cc_final: 0.7729 (mp0) REVERT: a 499 VAL cc_start: 0.9082 (t) cc_final: 0.8839 (p) REVERT: a 600 PHE cc_start: 0.8389 (t80) cc_final: 0.8138 (t80) REVERT: b 29 LYS cc_start: 0.9401 (tmtt) cc_final: 0.8951 (tmtt) REVERT: b 70 GLN cc_start: 0.9316 (mt0) cc_final: 0.8944 (mt0) REVERT: b 159 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7792 (mtmt) REVERT: b 548 ASN cc_start: 0.8307 (p0) cc_final: 0.7397 (m-40) REVERT: c 127 TRP cc_start: 0.8155 (t60) cc_final: 0.7680 (t60) REVERT: d 63 GLU cc_start: 0.8392 (tp30) cc_final: 0.8047 (tp30) REVERT: d 79 ASN cc_start: 0.8814 (m-40) cc_final: 0.8398 (p0) REVERT: d 127 TRP cc_start: 0.8380 (t-100) cc_final: 0.8018 (t-100) REVERT: d 128 ARG cc_start: 0.9437 (pmt-80) cc_final: 0.9113 (pmt-80) REVERT: d 159 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8179 (mtmt) REVERT: d 203 GLU cc_start: 0.8276 (tt0) cc_final: 0.8005 (tt0) REVERT: d 226 ASP cc_start: 0.8199 (m-30) cc_final: 0.7939 (m-30) REVERT: d 511 ASN cc_start: 0.8798 (t0) cc_final: 0.8567 (t0) REVERT: d 547 ASN cc_start: 0.7027 (t0) cc_final: 0.6645 (p0) REVERT: d 574 LEU cc_start: 0.9344 (tp) cc_final: 0.9045 (tp) REVERT: d 608 TYR cc_start: 0.8544 (m-10) cc_final: 0.7992 (m-10) REVERT: d 611 ASP cc_start: 0.8194 (m-30) cc_final: 0.7978 (m-30) REVERT: e 79 ASN cc_start: 0.8694 (m-40) cc_final: 0.8474 (p0) REVERT: e 125 ASP cc_start: 0.8563 (t0) cc_final: 0.8279 (m-30) REVERT: e 214 GLU cc_start: 0.9078 (pp20) cc_final: 0.8805 (pp20) REVERT: e 511 ASN cc_start: 0.8611 (t0) cc_final: 0.8145 (t0) REVERT: e 513 PHE cc_start: 0.8975 (m-80) cc_final: 0.7489 (m-80) REVERT: e 548 ASN cc_start: 0.8562 (p0) cc_final: 0.8011 (m110) REVERT: f 79 ASN cc_start: 0.8928 (m110) cc_final: 0.8622 (p0) REVERT: f 100 GLN cc_start: 0.8149 (mt0) cc_final: 0.7820 (mp10) REVERT: f 124 PHE cc_start: 0.8022 (t80) cc_final: 0.7543 (t80) REVERT: f 548 ASN cc_start: 0.7435 (m110) cc_final: 0.7160 (p0) REVERT: f 601 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8770 (mmmm) REVERT: g 63 GLU cc_start: 0.7768 (tp30) cc_final: 0.7495 (tp30) REVERT: g 79 ASN cc_start: 0.8849 (m-40) cc_final: 0.8360 (p0) REVERT: g 127 TRP cc_start: 0.8475 (t-100) cc_final: 0.8225 (t60) REVERT: g 213 PHE cc_start: 0.9015 (m-10) cc_final: 0.8741 (m-80) REVERT: g 297 ASN cc_start: 0.8943 (t0) cc_final: 0.8702 (t0) REVERT: g 600 PHE cc_start: 0.8421 (t80) cc_final: 0.7901 (t80) REVERT: g 608 TYR cc_start: 0.8488 (m-10) cc_final: 0.8177 (m-10) REVERT: g 611 ASP cc_start: 0.9170 (t0) cc_final: 0.8947 (t0) REVERT: g 615 LEU cc_start: 0.9101 (pp) cc_final: 0.8724 (tp) REVERT: h 63 GLU cc_start: 0.8510 (tp30) cc_final: 0.8057 (tp30) REVERT: h 79 ASN cc_start: 0.8743 (m110) cc_final: 0.8370 (p0) REVERT: h 307 ARG cc_start: 0.8051 (ttt-90) cc_final: 0.7384 (tmm-80) REVERT: h 511 ASN cc_start: 0.8969 (t0) cc_final: 0.8660 (t0) REVERT: h 548 ASN cc_start: 0.7461 (m110) cc_final: 0.7130 (p0) REVERT: i 63 GLU cc_start: 0.8359 (tp30) cc_final: 0.8098 (tp30) REVERT: i 136 LEU cc_start: 0.9085 (pp) cc_final: 0.8729 (pp) REVERT: i 160 TYR cc_start: 0.9079 (t80) cc_final: 0.8779 (t80) REVERT: i 307 ARG cc_start: 0.6923 (tpm170) cc_final: 0.6279 (tmm-80) REVERT: i 511 ASN cc_start: 0.9162 (t0) cc_final: 0.8092 (t0) REVERT: i 513 PHE cc_start: 0.8448 (m-80) cc_final: 0.7634 (m-80) REVERT: i 548 ASN cc_start: 0.7798 (m110) cc_final: 0.7349 (p0) REVERT: i 596 TRP cc_start: 0.8797 (t-100) cc_final: 0.8343 (t-100) REVERT: i 608 TYR cc_start: 0.8618 (m-10) cc_final: 0.7840 (m-10) REVERT: j 40 ARG cc_start: 0.7770 (tpt-90) cc_final: 0.7524 (tpt170) REVERT: j 63 GLU cc_start: 0.8133 (tp30) cc_final: 0.7851 (tp30) REVERT: j 70 GLN cc_start: 0.9117 (mt0) cc_final: 0.8801 (mt0) REVERT: j 125 ASP cc_start: 0.8793 (t70) cc_final: 0.8466 (m-30) REVERT: j 127 TRP cc_start: 0.8447 (t-100) cc_final: 0.8128 (t-100) REVERT: j 129 ASN cc_start: 0.9101 (t0) cc_final: 0.8780 (p0) REVERT: j 304 LEU cc_start: 0.8931 (pp) cc_final: 0.8686 (pp) REVERT: k 90 TRP cc_start: 0.7436 (t-100) cc_final: 0.6464 (t-100) REVERT: k 128 ARG cc_start: 0.9475 (pmt-80) cc_final: 0.9014 (pmt-80) REVERT: k 214 GLU cc_start: 0.8980 (pp20) cc_final: 0.8722 (pp20) REVERT: k 499 VAL cc_start: 0.8982 (t) cc_final: 0.8747 (p) REVERT: k 535 GLU cc_start: 0.8533 (tp30) cc_final: 0.8072 (tp30) REVERT: l 70 GLN cc_start: 0.9058 (mt0) cc_final: 0.8624 (mt0) REVERT: l 79 ASN cc_start: 0.8722 (m110) cc_final: 0.8464 (p0) REVERT: l 128 ARG cc_start: 0.9292 (pmt-80) cc_final: 0.8889 (pmt-80) REVERT: l 160 TYR cc_start: 0.9287 (t80) cc_final: 0.8839 (t80) outliers start: 4 outliers final: 0 residues processed: 836 average time/residue: 0.2292 time to fit residues: 305.2212 Evaluate side-chains 637 residues out of total 4140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 122 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 253 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 394 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 44 HIS ** a 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 515 HIS b 31 HIS ** b 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 511 ASN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 511 ASN ** g 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 HIS l 551 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.084504 restraints weight = 96400.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.086780 restraints weight = 59076.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088143 restraints weight = 43612.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089034 restraints weight = 36458.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089503 restraints weight = 32750.425| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40644 Z= 0.136 Angle : 0.647 10.425 55284 Z= 0.325 Chirality : 0.042 0.231 6048 Planarity : 0.005 0.063 7176 Dihedral : 4.291 23.924 5580 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % 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: 1.33 (0.12), residues: 4920 helix: 2.11 (0.10), residues: 2796 sheet: 0.35 (0.21), residues: 600 loop : -1.27 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 128 TYR 0.049 0.001 TYR l 608 PHE 0.048 0.001 PHE a 616 TRP 0.061 0.002 TRP l 127 HIS 0.010 0.001 HIS k 236 Details of bonding type rmsd covalent geometry : bond 0.00310 (40644) covalent geometry : angle 0.64719 (55284) hydrogen bonds : bond 0.03693 ( 2314) hydrogen bonds : angle 4.07845 ( 6732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7484.56 seconds wall clock time: 129 minutes 22.36 seconds (7762.36 seconds total)