Starting phenix.real_space_refine on Sat Oct 31 01:42:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygb_72919/10_2026/9ygb_72919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygb_72919/10_2026/9ygb_72919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygb_72919/10_2026/9ygb_72919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygb_72919/10_2026/9ygb_72919.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygb_72919/10_2026/9ygb_72919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygb_72919/10_2026/9ygb_72919.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 105 5.16 5 C 24510 2.51 5 N 7056 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39159 Number of models: 1 Model: "" Number of chains: 27 Chain: "F" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "E" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 521 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "A" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6283 Classifications: {'peptide': 812} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 764} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "B" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain: "S" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "W" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Chain: "U" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 521 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "I" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6283 Classifications: {'peptide': 812} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 764} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain: "T" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "X" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Chain: "V" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "R" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 521 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "J" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6283 Classifications: {'peptide': 812} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 764} Chain: "P" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "L" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12663 SG CYS B 178 98.859 82.507 123.973 1.00 44.85 S ATOM 12833 SG CYS B 201 93.611 86.541 123.996 1.00 44.19 S ATOM 12551 SG CYS B 165 92.749 80.180 123.397 1.00 38.07 S ATOM 12879 SG CYS B 208 95.584 83.422 118.773 1.00 52.27 S ATOM 25708 SG CYS K 178 67.899 18.463 123.961 1.00 44.85 S ATOM 25878 SG CYS K 201 74.029 20.913 123.988 1.00 44.19 S ATOM 25596 SG CYS K 165 68.985 24.899 123.373 1.00 38.07 S ATOM 25924 SG CYS K 208 70.358 20.859 118.755 1.00 52.27 S ATOM 38753 SG CYS L 178 27.911 77.270 123.958 1.00 44.85 S ATOM 38923 SG CYS L 201 27.023 70.717 124.000 1.00 44.19 S ATOM 38641 SG CYS L 165 32.994 73.162 123.364 1.00 38.07 S ATOM 38969 SG CYS L 208 28.788 73.942 118.771 1.00 52.27 S Time building chain proxies: 7.84, per 1000 atoms: 0.20 Number of scatterers: 39159 At special positions: 0 Unit cell: (123.2, 127.6, 260.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 105 16.00 O 7476 8.00 N 7056 7.00 C 24510 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 178 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 208 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 165 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 201 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 178 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 208 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 165 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 201 " pdb=" SF4 L 301 " pdb="FE1 SF4 L 301 " - pdb=" SG CYS L 178 " pdb="FE4 SF4 L 301 " - pdb=" SG CYS L 208 " pdb="FE3 SF4 L 301 " - pdb=" SG CYS L 165 " pdb="FE2 SF4 L 301 " - pdb=" SG CYS L 201 " Number of angles added : 36 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9132 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 79 sheets defined 15.4% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'F' and resid 579 through 598 Processing helix chain 'F' and resid 603 through 610 Processing helix chain 'H' and resid 76 through 88 removed outlier: 3.668A pdb=" N VAL H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 69 Proline residue: C 60 - end of helix removed outlier: 3.674A pdb=" N HIS C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 3.615A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.761A pdb=" N VAL A 303 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 removed outlier: 4.146A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.790A pdb=" N ILE A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.677A pdb=" N THR A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 removed outlier: 3.658A pdb=" N GLY A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 426 through 434 removed outlier: 4.057A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.084A pdb=" N ALA A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'D' and resid 55 through 68 Proline residue: D 60 - end of helix removed outlier: 3.622A pdb=" N HIS D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 24 through 27 Processing helix chain 'B' and resid 79 through 88 removed outlier: 3.514A pdb=" N ALA B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 4.154A pdb=" N VAL B 92 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.514A pdb=" N ASP B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.509A pdb=" N ARG B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'S' and resid 580 through 598 Processing helix chain 'S' and resid 603 through 610 Processing helix chain 'W' and resid 76 through 88 removed outlier: 3.662A pdb=" N VAL W 80 " --> pdb=" O LEU W 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 69 Proline residue: M 60 - end of helix removed outlier: 3.684A pdb=" N HIS M 68 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 87 removed outlier: 3.617A pdb=" N VAL U 80 " --> pdb=" O LEU U 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 133 Processing helix chain 'Q' and resid 138 through 143 Processing helix chain 'Q' and resid 154 through 158 Processing helix chain 'Q' and resid 196 through 200 removed outlier: 3.537A pdb=" N LEU Q 200 " --> pdb=" O GLU Q 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 233 through 235 No H-bonds generated for 'chain 'I' and resid 233 through 235' Processing helix chain 'I' and resid 278 through 289 Processing helix chain 'I' and resid 299 through 303 removed outlier: 3.765A pdb=" N VAL I 303 " --> pdb=" O ALA I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 316 removed outlier: 4.137A pdb=" N LEU I 308 " --> pdb=" O ASP I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 353 removed outlier: 3.786A pdb=" N ILE I 352 " --> pdb=" O ASP I 348 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 383 removed outlier: 3.671A pdb=" N THR I 383 " --> pdb=" O PRO I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 416 removed outlier: 3.646A pdb=" N GLY I 416 " --> pdb=" O PRO I 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 413 through 416' Processing helix chain 'I' and resid 426 through 434 removed outlier: 4.002A pdb=" N ARG I 432 " --> pdb=" O ARG I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 465 Processing helix chain 'I' and resid 474 through 478 Processing helix chain 'I' and resid 490 through 495 Processing helix chain 'I' and resid 597 through 604 removed outlier: 4.076A pdb=" N ALA I 601 " --> pdb=" O SER I 597 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN I 604 " --> pdb=" O ASP I 600 " (cutoff:3.500A) Processing helix chain 'I' and resid 763 through 767 Processing helix chain 'O' and resid 55 through 68 Proline residue: O 60 - end of helix removed outlier: 3.645A pdb=" N HIS O 68 " --> pdb=" O PHE O 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 7 Processing helix chain 'K' and resid 24 through 27 Processing helix chain 'K' and resid 79 through 88 removed outlier: 3.519A pdb=" N ALA K 83 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 removed outlier: 4.219A pdb=" N VAL K 92 " --> pdb=" O ASP K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 104 through 106 No H-bonds generated for 'chain 'K' and resid 104 through 106' Processing helix chain 'K' and resid 107 through 111 Processing helix chain 'K' and resid 165 through 170 Processing helix chain 'K' and resid 195 through 199 removed outlier: 3.514A pdb=" N ASP K 199 " --> pdb=" O PRO K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 213 removed outlier: 3.518A pdb=" N ARG K 211 " --> pdb=" O ASP K 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 580 through 598 Processing helix chain 'T' and resid 603 through 610 Processing helix chain 'X' and resid 76 through 88 removed outlier: 3.665A pdb=" N VAL X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 69 Proline residue: N 60 - end of helix removed outlier: 3.696A pdb=" N HIS N 68 " --> pdb=" O PHE N 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 87 removed outlier: 3.606A pdb=" N VAL V 80 " --> pdb=" O LEU V 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 133 Processing helix chain 'R' and resid 138 through 143 Processing helix chain 'R' and resid 154 through 158 Processing helix chain 'R' and resid 198 through 200 No H-bonds generated for 'chain 'R' and resid 198 through 200' Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 233 through 235 No H-bonds generated for 'chain 'J' and resid 233 through 235' Processing helix chain 'J' and resid 278 through 289 Processing helix chain 'J' and resid 299 through 303 removed outlier: 3.769A pdb=" N VAL J 303 " --> pdb=" O ALA J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 316 removed outlier: 4.092A pdb=" N LEU J 308 " --> pdb=" O ASP J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 352 removed outlier: 3.775A pdb=" N ILE J 352 " --> pdb=" O ASP J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 383 removed outlier: 3.691A pdb=" N THR J 383 " --> pdb=" O PRO J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 416 removed outlier: 3.628A pdb=" N GLY J 416 " --> pdb=" O PRO J 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 413 through 416' Processing helix chain 'J' and resid 426 through 434 removed outlier: 4.045A pdb=" N ARG J 432 " --> pdb=" O ARG J 428 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 465 Processing helix chain 'J' and resid 474 through 478 Processing helix chain 'J' and resid 490 through 495 Processing helix chain 'J' and resid 597 through 604 removed outlier: 4.076A pdb=" N ALA J 601 " --> pdb=" O SER J 597 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN J 604 " --> pdb=" O ASP J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 763 through 767 Processing helix chain 'P' and resid 55 through 68 Proline residue: P 60 - end of helix removed outlier: 3.628A pdb=" N HIS P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 24 through 27 removed outlier: 3.541A pdb=" N GLY L 27 " --> pdb=" O THR L 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 24 through 27' Processing helix chain 'L' and resid 79 through 88 removed outlier: 3.523A pdb=" N ALA L 83 " --> pdb=" O GLY L 79 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 92 removed outlier: 4.226A pdb=" N VAL L 92 " --> pdb=" O ASP L 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 89 through 92' Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 165 through 170 Processing helix chain 'L' and resid 195 through 199 removed outlier: 3.503A pdb=" N ASP L 199 " --> pdb=" O PRO L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 213 Processing sheet with id=AA1, first strand: chain 'H' and resid 9 through 14 removed outlier: 4.627A pdb=" N ILE H 10 " --> pdb=" O ILE H 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 28 current: chain 'H' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 65 through 71 current: chain 'H' and resid 125 through 134 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 125 through 134 current: chain 'H' and resid 146 through 153 Processing sheet with id=AA2, first strand: chain 'H' and resid 41 through 45 removed outlier: 5.030A pdb=" N LEU H 60 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE H 44 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS H 58 " --> pdb=" O ILE H 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'C' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 54 current: chain 'C' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 87 current: chain 'C' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 110 current: chain 'D' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 54 current: chain 'D' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 87 current: chain 'D' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 100 through 110 current: chain 'M' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 43 through 54 current: chain 'M' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 83 through 87 current: chain 'M' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 100 through 110 current: chain 'O' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 43 through 54 current: chain 'O' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 83 through 87 current: chain 'O' and resid 100 through 109 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 100 through 109 current: chain 'N' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 43 through 54 current: chain 'N' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 83 through 87 current: chain 'N' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 100 through 110 current: chain 'P' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 43 through 54 current: chain 'P' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 83 through 87 current: chain 'P' and resid 100 through 110 Processing sheet with id=AA5, first strand: chain 'C' and resid 23 through 27 Processing sheet with id=AA6, first strand: chain 'G' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 24 through 27 current: chain 'G' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 65 through 71 current: chain 'G' and resid 125 through 134 removed outlier: 6.958A pdb=" N THR G 150 " --> pdb=" O SER G 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 41 through 45 removed outlier: 4.634A pdb=" N ASP G 42 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 180 Processing sheet with id=AB1, first strand: chain 'E' and resid 182 through 185 Processing sheet with id=AB2, first strand: chain 'E' and resid 188 through 196 removed outlier: 6.863A pdb=" N LEU A 34 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA E 192 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 32 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE E 194 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG A 30 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 100 removed outlier: 5.767A pdb=" N VAL A 90 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A 215 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN A 92 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL A 213 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 94 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N THR A 211 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 96 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 209 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET A 205 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL A 207 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER A 123 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 209 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.513A pdb=" N ILE A 147 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU A 156 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 149 " --> pdb=" O TRP A 154 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TRP A 154 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.568A pdb=" N GLN A 128 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AB7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.561A pdb=" N SER A 262 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AB9, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AC1, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AC2, first strand: chain 'A' and resid 374 through 378 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 374 through 378 current: chain 'A' and resid 467 through 473 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 467 through 473 current: chain 'A' and resid 572 through 583 removed outlier: 6.879A pdb=" N THR A 590 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 579 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A 588 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 581 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 586 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 419 through 425 removed outlier: 6.534A pdb=" N LEU A 405 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 440 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 407 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 499 through 501 removed outlier: 5.217A pdb=" N GLN A 561 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 527 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER A 547 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL A 541 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 504 " --> pdb=" O THR A 511 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 628 through 636 Processing sheet with id=AC6, first strand: chain 'A' and resid 656 through 663 removed outlier: 6.351A pdb=" N TYR A 657 " --> pdb=" O ARG A 673 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG A 673 " --> pdb=" O TYR A 657 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 659 " --> pdb=" O VAL A 671 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 669 through 674 current: chain 'A' and resid 706 through 707 Processing sheet with id=AC7, first strand: chain 'A' and resid 725 through 731 removed outlier: 3.771A pdb=" N TYR A 725 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 734 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 768 through 774 removed outlier: 7.032A pdb=" N ILE A 754 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 772 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 752 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA A 774 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA A 750 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 798 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR A 752 " --> pdb=" O ARG A 796 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 796 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 754 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG A 794 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A 756 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 792 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 24 through 27 removed outlier: 8.131A pdb=" N LEU B 15 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY D 37 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N ARG B 17 " --> pdb=" O GLY D 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 34 current: chain 'B' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 47 through 51 current: chain 'B' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'B' and resid 124 through 136 removed outlier: 6.490A pdb=" N GLU B 144 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 142 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 135 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 140 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 9 through 14 removed outlier: 4.637A pdb=" N ILE W 10 " --> pdb=" O ILE W 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 24 through 28 current: chain 'W' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 65 through 71 current: chain 'W' and resid 125 through 134 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 125 through 134 current: chain 'W' and resid 146 through 153 Processing sheet with id=AD2, first strand: chain 'W' and resid 41 through 45 removed outlier: 5.066A pdb=" N LEU W 60 " --> pdb=" O ASP W 42 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE W 44 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS W 58 " --> pdb=" O ILE W 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 109 through 110 Processing sheet with id=AD4, first strand: chain 'M' and resid 23 through 27 Processing sheet with id=AD5, first strand: chain 'U' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 24 through 27 current: chain 'U' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 65 through 71 current: chain 'U' and resid 125 through 134 removed outlier: 6.952A pdb=" N THR U 150 " --> pdb=" O SER U 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 41 through 45 removed outlier: 4.629A pdb=" N ASP U 42 " --> pdb=" O GLY U 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 109 through 110 Processing sheet with id=AD8, first strand: chain 'Q' and resid 178 through 180 Processing sheet with id=AD9, first strand: chain 'Q' and resid 182 through 185 removed outlier: 3.532A pdb=" N ALA I 245 " --> pdb=" O ARG Q 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 188 through 195 removed outlier: 6.861A pdb=" N LEU I 34 " --> pdb=" O ILE Q 190 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA Q 192 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS I 32 " --> pdb=" O ALA Q 192 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE Q 194 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG I 30 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA I 224 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 88 through 100 removed outlier: 5.782A pdb=" N VAL I 90 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP I 215 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN I 92 " --> pdb=" O VAL I 213 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL I 213 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU I 94 " --> pdb=" O THR I 211 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR I 211 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL I 96 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA I 209 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET I 205 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL I 207 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER I 123 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 209 " --> pdb=" O ARG I 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 106 through 110 removed outlier: 6.529A pdb=" N ILE I 147 " --> pdb=" O GLU I 156 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU I 156 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL I 149 " --> pdb=" O TRP I 154 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TRP I 154 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 136 through 137 removed outlier: 3.586A pdb=" N GLN I 128 " --> pdb=" O ALA I 202 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 250 through 253 Processing sheet with id=AE6, first strand: chain 'I' and resid 256 through 257 removed outlier: 3.563A pdb=" N SER I 262 " --> pdb=" O ASP I 257 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 318 through 320 Processing sheet with id=AE8, first strand: chain 'I' and resid 340 through 341 Processing sheet with id=AE9, first strand: chain 'I' and resid 355 through 359 Processing sheet with id=AF1, first strand: chain 'I' and resid 374 through 378 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 374 through 378 current: chain 'I' and resid 467 through 473 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 467 through 473 current: chain 'I' and resid 572 through 583 removed outlier: 6.877A pdb=" N THR I 590 " --> pdb=" O MET I 577 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE I 579 " --> pdb=" O GLU I 588 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU I 588 " --> pdb=" O ILE I 579 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG I 581 " --> pdb=" O LEU I 586 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU I 586 " --> pdb=" O ARG I 581 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 419 through 425 removed outlier: 6.535A pdb=" N LEU I 405 " --> pdb=" O LEU I 438 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE I 440 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU I 407 " --> pdb=" O ILE I 440 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 499 through 501 removed outlier: 5.183A pdb=" N GLN I 561 " --> pdb=" O ASN I 527 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN I 527 " --> pdb=" O GLN I 561 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER I 547 " --> pdb=" O GLN I 539 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL I 541 " --> pdb=" O VAL I 545 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL I 545 " --> pdb=" O VAL I 541 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA I 504 " --> pdb=" O THR I 511 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 628 through 636 Processing sheet with id=AF5, first strand: chain 'I' and resid 656 through 663 removed outlier: 6.370A pdb=" N TYR I 657 " --> pdb=" O ARG I 673 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG I 673 " --> pdb=" O TYR I 657 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA I 659 " --> pdb=" O VAL I 671 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 669 through 674 current: chain 'I' and resid 706 through 707 Processing sheet with id=AF6, first strand: chain 'I' and resid 725 through 731 removed outlier: 3.792A pdb=" N TYR I 725 " --> pdb=" O GLY I 740 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 768 through 774 removed outlier: 7.019A pdb=" N ILE I 754 " --> pdb=" O LEU I 770 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU I 772 " --> pdb=" O THR I 752 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR I 752 " --> pdb=" O LEU I 772 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA I 774 " --> pdb=" O ALA I 750 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA I 750 " --> pdb=" O ALA I 774 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE I 798 " --> pdb=" O ALA I 750 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR I 752 " --> pdb=" O ARG I 796 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG I 796 " --> pdb=" O THR I 752 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE I 754 " --> pdb=" O ARG I 794 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG I 794 " --> pdb=" O ILE I 754 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN I 756 " --> pdb=" O ALA I 792 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA I 792 " --> pdb=" O GLN I 756 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 24 through 27 removed outlier: 8.090A pdb=" N LEU K 15 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY O 37 " --> pdb=" O LEU K 15 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ARG K 17 " --> pdb=" O GLY O 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 30 through 34 current: chain 'K' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 47 through 51 current: chain 'K' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 71 through 75 current: chain 'K' and resid 124 through 136 removed outlier: 6.507A pdb=" N GLU K 131 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER K 146 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS K 133 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU K 144 " --> pdb=" O LYS K 133 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 9 through 14 removed outlier: 4.645A pdb=" N ILE X 10 " --> pdb=" O ILE X 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 24 through 28 current: chain 'X' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 65 through 71 current: chain 'X' and resid 125 through 134 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 125 through 134 current: chain 'X' and resid 146 through 153 Processing sheet with id=AG1, first strand: chain 'X' and resid 41 through 45 removed outlier: 5.045A pdb=" N LEU X 60 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE X 44 " --> pdb=" O LYS X 58 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS X 58 " --> pdb=" O ILE X 44 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'X' and resid 109 through 110 Processing sheet with id=AG3, first strand: chain 'N' and resid 23 through 27 Processing sheet with id=AG4, first strand: chain 'V' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 24 through 27 current: chain 'V' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 65 through 71 current: chain 'V' and resid 125 through 134 removed outlier: 6.960A pdb=" N THR V 150 " --> pdb=" O SER V 133 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 41 through 45 removed outlier: 4.634A pdb=" N ASP V 42 " --> pdb=" O GLY V 59 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 109 through 110 Processing sheet with id=AG7, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AG8, first strand: chain 'R' and resid 182 through 185 removed outlier: 3.500A pdb=" N ALA J 245 " --> pdb=" O ARG R 183 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 188 through 196 removed outlier: 6.866A pdb=" N LEU J 34 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA R 192 " --> pdb=" O LYS J 32 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS J 32 " --> pdb=" O ALA R 192 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE R 194 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG J 30 " --> pdb=" O ILE R 194 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA J 224 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 88 through 100 removed outlier: 5.785A pdb=" N VAL J 90 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP J 215 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASN J 92 " --> pdb=" O VAL J 213 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL J 213 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU J 94 " --> pdb=" O THR J 211 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR J 211 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL J 96 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA J 209 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET J 205 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL J 207 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER J 123 " --> pdb=" O VAL J 207 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA J 209 " --> pdb=" O ARG J 121 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 106 through 110 removed outlier: 6.502A pdb=" N ILE J 147 " --> pdb=" O GLU J 156 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU J 156 " --> pdb=" O ILE J 147 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL J 149 " --> pdb=" O TRP J 154 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TRP J 154 " --> pdb=" O VAL J 149 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 136 through 137 removed outlier: 3.583A pdb=" N GLN J 128 " --> pdb=" O ALA J 202 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 250 through 253 Processing sheet with id=AH5, first strand: chain 'J' and resid 256 through 257 removed outlier: 3.554A pdb=" N SER J 262 " --> pdb=" O ASP J 257 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 318 through 320 Processing sheet with id=AH7, first strand: chain 'J' and resid 340 through 341 Processing sheet with id=AH8, first strand: chain 'J' and resid 355 through 359 Processing sheet with id=AH9, first strand: chain 'J' and resid 374 through 378 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 374 through 378 current: chain 'J' and resid 467 through 473 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 467 through 473 current: chain 'J' and resid 572 through 583 removed outlier: 6.896A pdb=" N THR J 590 " --> pdb=" O MET J 577 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE J 579 " --> pdb=" O GLU J 588 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU J 588 " --> pdb=" O ILE J 579 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG J 581 " --> pdb=" O LEU J 586 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU J 586 " --> pdb=" O ARG J 581 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 419 through 425 removed outlier: 6.534A pdb=" N LEU J 405 " --> pdb=" O LEU J 438 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE J 440 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU J 407 " --> pdb=" O ILE J 440 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 499 through 501 removed outlier: 5.204A pdb=" N GLN J 561 " --> pdb=" O ASN J 527 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN J 527 " --> pdb=" O GLN J 561 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER J 547 " --> pdb=" O GLN J 539 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL J 541 " --> pdb=" O VAL J 545 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL J 545 " --> pdb=" O VAL J 541 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J 504 " --> pdb=" O THR J 511 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 628 through 636 Processing sheet with id=AI4, first strand: chain 'J' and resid 656 through 663 removed outlier: 6.355A pdb=" N TYR J 657 " --> pdb=" O ARG J 673 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG J 673 " --> pdb=" O TYR J 657 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA J 659 " --> pdb=" O VAL J 671 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 669 through 674 current: chain 'J' and resid 706 through 707 Processing sheet with id=AI5, first strand: chain 'J' and resid 725 through 731 removed outlier: 3.795A pdb=" N TYR J 725 " --> pdb=" O GLY J 740 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 768 through 774 removed outlier: 7.035A pdb=" N ILE J 754 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU J 772 " --> pdb=" O THR J 752 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR J 752 " --> pdb=" O LEU J 772 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ALA J 774 " --> pdb=" O ALA J 750 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA J 750 " --> pdb=" O ALA J 774 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE J 798 " --> pdb=" O ALA J 750 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR J 752 " --> pdb=" O ARG J 796 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG J 796 " --> pdb=" O THR J 752 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE J 754 " --> pdb=" O ARG J 794 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG J 794 " --> pdb=" O ILE J 754 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN J 756 " --> pdb=" O ALA J 792 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA J 792 " --> pdb=" O GLN J 756 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 24 through 27 removed outlier: 8.109A pdb=" N LEU L 15 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY P 37 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ARG L 17 " --> pdb=" O GLY P 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 30 through 34 current: chain 'L' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 47 through 51 current: chain 'L' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 71 through 75 current: chain 'L' and resid 124 through 136 removed outlier: 6.474A pdb=" N GLU L 144 " --> pdb=" O GLU L 131 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS L 133 " --> pdb=" O THR L 142 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR L 142 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA L 135 " --> pdb=" O GLN L 140 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN L 140 " --> pdb=" O ALA L 135 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2307 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: 9.82 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 17643 1.44 - 1.65: 22260 1.65 - 1.86: 147 1.86 - 2.07: 0 2.07 - 2.28: 36 Bond restraints: 40086 Sorted by residual: bond pdb=" C PHE G 135 " pdb=" N PRO G 136 " ideal model delta sigma weight residual 1.326 1.346 -0.020 1.44e-02 4.82e+03 1.93e+00 bond pdb=" C PRO X 15 " pdb=" N PRO X 16 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.26e-02 6.30e+03 1.89e+00 bond pdb=" C PHE V 135 " pdb=" N PRO V 136 " ideal model delta sigma weight residual 1.326 1.346 -0.019 1.44e-02 4.82e+03 1.83e+00 bond pdb=" C PHE U 135 " pdb=" N PRO U 136 " ideal model delta sigma weight residual 1.326 1.346 -0.019 1.44e-02 4.82e+03 1.82e+00 bond pdb=" CA PRO I 719 " pdb=" C PRO I 719 " ideal model delta sigma weight residual 1.514 1.522 -0.007 5.50e-03 3.31e+04 1.81e+00 ... (remaining 40081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 54054 2.45 - 4.90: 486 4.90 - 7.35: 9 7.35 - 9.80: 0 9.80 - 12.25: 6 Bond angle restraints: 54555 Sorted by residual: angle pdb=" CA ASN J 197 " pdb=" C ASN J 197 " pdb=" N ASN J 198 " ideal model delta sigma weight residual 118.27 123.53 -5.26 1.59e+00 3.96e-01 1.09e+01 angle pdb=" CA ASN I 197 " pdb=" C ASN I 197 " pdb=" N ASN I 198 " ideal model delta sigma weight residual 118.27 123.50 -5.23 1.59e+00 3.96e-01 1.08e+01 angle pdb=" CA ASN A 197 " pdb=" C ASN A 197 " pdb=" N ASN A 198 " ideal model delta sigma weight residual 118.27 123.47 -5.20 1.59e+00 3.96e-01 1.07e+01 angle pdb=" N GLY B 13 " pdb=" CA GLY B 13 " pdb=" C GLY B 13 " ideal model delta sigma weight residual 110.29 114.33 -4.04 1.28e+00 6.10e-01 9.95e+00 angle pdb=" N GLY K 13 " pdb=" CA GLY K 13 " pdb=" C GLY K 13 " ideal model delta sigma weight residual 110.20 114.34 -4.14 1.32e+00 5.74e-01 9.84e+00 ... (remaining 54550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 22304 17.75 - 35.49: 1031 35.49 - 53.24: 233 53.24 - 70.98: 77 70.98 - 88.73: 16 Dihedral angle restraints: 23661 sinusoidal: 9330 harmonic: 14331 Sorted by residual: dihedral pdb=" CA PRO A 22 " pdb=" C PRO A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PRO J 22 " pdb=" C PRO J 22 " pdb=" N ASP J 23 " pdb=" CA ASP J 23 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO I 22 " pdb=" C PRO I 22 " pdb=" N ASP I 23 " pdb=" CA ASP I 23 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 23658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3427 0.030 - 0.060: 1537 0.060 - 0.090: 464 0.090 - 0.119: 394 0.119 - 0.149: 49 Chirality restraints: 5871 Sorted by residual: chirality pdb=" CA ILE A 616 " pdb=" N ILE A 616 " pdb=" C ILE A 616 " pdb=" CB ILE A 616 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE J 616 " pdb=" N ILE J 616 " pdb=" C ILE J 616 " pdb=" CB ILE J 616 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE J 798 " pdb=" N ILE J 798 " pdb=" C ILE J 798 " pdb=" CB ILE J 798 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 5868 not shown) Planarity restraints: 7266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 379 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO I 380 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO I 380 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 380 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 379 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO J 380 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 380 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 380 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 379 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 380 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.025 5.00e-02 4.00e+02 ... (remaining 7263 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8239 2.79 - 3.32: 33243 3.32 - 3.84: 60948 3.84 - 4.37: 75708 4.37 - 4.90: 134207 Nonbonded interactions: 312345 Sorted by model distance: nonbonded pdb=" NH1 ARG B 174 " pdb=" OD2 ASP B 199 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG K 174 " pdb=" OD2 ASP K 199 " model vdw 2.261 3.120 nonbonded pdb=" NH1 ARG L 174 " pdb=" OD2 ASP L 199 " model vdw 2.266 3.120 nonbonded pdb=" NH2 ARG A 248 " pdb=" OD1 ASP A 285 " model vdw 2.305 3.120 nonbonded pdb=" O GLY E 148 " pdb=" OG1 THR J 441 " model vdw 2.312 3.040 ... (remaining 312340 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 'I' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 41.510 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 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 : 0.004 0.039 40098 Z= 0.159 Angle : 0.605 12.255 54591 Z= 0.324 Chirality : 0.044 0.149 5871 Planarity : 0.005 0.046 7266 Dihedral : 11.851 88.729 14529 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.37 % Allowed : 2.23 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.11), residues: 5040 helix: -0.05 (0.21), residues: 573 sheet: 0.67 (0.13), residues: 1545 loop : -0.34 (0.10), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 249 TYR 0.013 0.001 TYR U 131 PHE 0.016 0.002 PHE B 33 TRP 0.014 0.001 TRP I 281 HIS 0.006 0.001 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (40086) covalent geometry : angle 0.59598 / 0.32 (54555) hydrogen bonds : bond 0.18422 / 12.29 ( 880) hydrogen bonds : angle 7.56960 / 5.35 ( 2307) metal coordination : bond 0.00475 / 0.31 ( 12) metal coordination : angle 4.08871 / 2.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 546 time to evaluate : 1.366 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: C 38 ASP cc_start: 0.8400 (m-30) cc_final: 0.8197 (m-30) REVERT: G 29 GLU cc_start: 0.7694 (mp0) cc_final: 0.7459 (mp0) REVERT: D 14 ASP cc_start: 0.8228 (p0) cc_final: 0.7954 (p0) REVERT: W 102 ASP cc_start: 0.7569 (m-30) cc_final: 0.7213 (m-30) REVERT: U 117 PHE cc_start: 0.8347 (m-80) cc_final: 0.8140 (m-80) REVERT: O 14 ASP cc_start: 0.8221 (p0) cc_final: 0.8006 (p0) REVERT: V 29 GLU cc_start: 0.7735 (mp0) cc_final: 0.7486 (mp0) REVERT: V 117 PHE cc_start: 0.8397 (m-80) cc_final: 0.8068 (m-80) REVERT: J 190 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8795 (ttm170) REVERT: L 167 TRP cc_start: 0.9445 (OUTLIER) cc_final: 0.8900 (m100) outliers start: 15 outliers final: 0 residues processed: 555 average time/residue: 0.9640 time to fit residues: 618.5369 Evaluate side-chains 322 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [432, 197, 388, 455, 215, 20, 132, 494, 261, 248, 207] chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.4980 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 2.9990 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 ASN G 43 GLN A 196 GLN A 259 GLN A 393 ASN A 399 GLN A 418 GLN D 89 GLN B 8 GLN S 593 ASN S 597 GLN W 43 GLN U 43 GLN U 142 ASN I 399 GLN I 418 GLN O 25 GLN K 8 GLN K 152 GLN T 597 GLN X 43 GLN X 142 ASN N 112 ASN V 43 GLN ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN J 399 GLN J 418 GLN P 89 GLN L 8 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.054184 restraints weight = 88932.255| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.72 r_work: 0.2547 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40098 Z= 0.136 Angle : 0.553 11.103 54591 Z= 0.285 Chirality : 0.044 0.160 5871 Planarity : 0.005 0.050 7266 Dihedral : 4.640 59.066 5574 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.17 % Allowed : 8.63 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.11), residues: 5040 helix: 0.41 (0.22), residues: 576 sheet: 0.54 (0.13), residues: 1638 loop : -0.35 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 519 TYR 0.014 0.001 TYR Q 161 PHE 0.017 0.001 PHE A 632 TRP 0.013 0.001 TRP K 143 HIS 0.005 0.001 HIS J 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (40086) covalent geometry : angle 0.54379 / 0.28 (54555) hydrogen bonds : bond 0.04077 / 2.79 ( 880) hydrogen bonds : angle 5.81540 / 4.14 ( 2307) metal coordination : bond 0.00555 / 0.40 ( 12) metal coordination : angle 3.92004 / 2.45 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8728 (mt0) REVERT: H 88 LYS cc_start: 0.8876 (tptm) cc_final: 0.8409 (tmmt) REVERT: C 38 ASP cc_start: 0.8483 (m-30) cc_final: 0.7911 (m-30) REVERT: G 87 GLU cc_start: 0.8644 (pp20) cc_final: 0.8387 (pp20) REVERT: G 88 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8209 (mmmm) REVERT: A 756 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: D 82 GLU cc_start: 0.8800 (mp0) cc_final: 0.8298 (mp0) REVERT: B 57 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8192 (ptp-110) REVERT: S 610 ASN cc_start: 0.8831 (m110) cc_final: 0.8389 (m-40) REVERT: W 88 LYS cc_start: 0.8920 (tptm) cc_final: 0.8358 (tmmt) REVERT: W 117 PHE cc_start: 0.8302 (m-80) cc_final: 0.7994 (m-80) REVERT: W 158 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7676 (tmtp) REVERT: W 162 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8433 (ttmt) REVERT: U 58 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8752 (tttt) REVERT: U 117 PHE cc_start: 0.8412 (m-80) cc_final: 0.7950 (m-80) REVERT: U 129 GLU cc_start: 0.7712 (pp20) cc_final: 0.7478 (pp20) REVERT: I 190 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8399 (ttm110) REVERT: I 246 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7733 (mtm-85) REVERT: I 584 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8846 (t0) REVERT: I 756 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: O 82 GLU cc_start: 0.8680 (mp0) cc_final: 0.8338 (mp0) REVERT: T 610 ASN cc_start: 0.8473 (m-40) cc_final: 0.8043 (m-40) REVERT: X 88 LYS cc_start: 0.8848 (tppp) cc_final: 0.7860 (tmmt) REVERT: X 117 PHE cc_start: 0.7999 (m-80) cc_final: 0.7709 (m-80) REVERT: X 158 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7674 (tmtp) REVERT: V 117 PHE cc_start: 0.8387 (m-80) cc_final: 0.7919 (m-80) REVERT: V 129 GLU cc_start: 0.7571 (pp20) cc_final: 0.7310 (pp20) REVERT: J 246 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7816 (mtm-85) REVERT: J 756 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: P 82 GLU cc_start: 0.8749 (mp0) cc_final: 0.8045 (mp0) REVERT: L 167 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.8379 (m100) outliers start: 48 outliers final: 13 residues processed: 374 average time/residue: 0.9533 time to fit residues: 414.4741 Evaluate side-chains 336 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain B residue 167 TRP Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 246 ARG Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain J residue 246 ARG Chi-restraints excluded: chain J residue 393 ASN Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [22, 435, 116, 87, 206, 417, 233, 68, 378, 470, 33] chunk 22 optimal weight: 1.9990 chunk 435 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 417 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 378 optimal weight: 0.9980 chunk 470 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 ASN G 43 GLN D 89 GLN S 597 GLN M 112 ASN U 43 GLN U 142 ASN O 25 GLN T 593 ASN T 597 GLN ** X 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 ASN V 43 GLN ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN J 8 HIS P 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.054120 restraints weight = 89269.323| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.74 r_work: 0.2549 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40098 Z= 0.129 Angle : 0.511 10.123 54591 Z= 0.261 Chirality : 0.043 0.156 5871 Planarity : 0.004 0.042 7266 Dihedral : 4.272 43.205 5570 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.20 % Allowed : 9.68 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.11), residues: 5040 helix: 0.64 (0.22), residues: 576 sheet: 0.47 (0.13), residues: 1680 loop : -0.30 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 182 TYR 0.014 0.001 TYR Q 161 PHE 0.013 0.001 PHE A 632 TRP 0.012 0.001 TRP J 283 HIS 0.004 0.001 HIS J 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (40086) covalent geometry : angle 0.50124 / 0.26 (54555) hydrogen bonds : bond 0.03606 / 2.45 ( 880) hydrogen bonds : angle 5.40308 / 3.85 ( 2307) metal coordination : bond 0.00428 / 0.29 ( 12) metal coordination : angle 3.93667 / 2.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 332 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8807 (mt0) REVERT: H 162 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (ttmm) REVERT: C 38 ASP cc_start: 0.8528 (m-30) cc_final: 0.7896 (m-30) REVERT: G 88 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8386 (mtpp) REVERT: G 129 GLU cc_start: 0.7510 (pp20) cc_final: 0.7267 (pp20) REVERT: E 161 TYR cc_start: 0.9040 (p90) cc_final: 0.8826 (p90) REVERT: D 82 GLU cc_start: 0.8872 (mp0) cc_final: 0.8280 (mp0) REVERT: S 597 GLN cc_start: 0.8072 (mt0) cc_final: 0.7783 (tt0) REVERT: S 610 ASN cc_start: 0.8929 (m110) cc_final: 0.8486 (m-40) REVERT: W 88 LYS cc_start: 0.8866 (tptm) cc_final: 0.8398 (tmmt) REVERT: W 123 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6208 (ptp-170) REVERT: W 129 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: W 158 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7735 (tmtp) REVERT: W 162 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8466 (ttpt) REVERT: U 84 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8896 (mp10) REVERT: U 88 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8216 (mmmm) REVERT: U 117 PHE cc_start: 0.8415 (m-80) cc_final: 0.7953 (m-80) REVERT: U 129 GLU cc_start: 0.7787 (pp20) cc_final: 0.7419 (pp20) REVERT: I 180 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8120 (pp20) REVERT: I 190 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8375 (ttm110) REVERT: I 584 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8899 (t0) REVERT: O 82 GLU cc_start: 0.8723 (mp0) cc_final: 0.8152 (mp0) REVERT: K 159 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7952 (mtp180) REVERT: T 610 ASN cc_start: 0.8570 (m-40) cc_final: 0.8136 (m-40) REVERT: X 129 GLU cc_start: 0.8093 (tt0) cc_final: 0.7574 (tm-30) REVERT: V 54 ARG cc_start: 0.8991 (mtt90) cc_final: 0.8764 (ttm-80) REVERT: V 117 PHE cc_start: 0.8412 (m-80) cc_final: 0.8035 (m-80) REVERT: V 129 GLU cc_start: 0.7655 (pp20) cc_final: 0.7251 (pp20) REVERT: J 584 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8823 (t0) REVERT: P 82 GLU cc_start: 0.8786 (mp0) cc_final: 0.8252 (mp0) REVERT: L 167 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.8420 (m100) outliers start: 49 outliers final: 14 residues processed: 361 average time/residue: 0.9649 time to fit residues: 403.2355 Evaluate side-chains 326 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 167 TRP Chi-restraints excluded: chain W residue 123 ARG Chi-restraints excluded: chain W residue 129 GLU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 614 THR Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 393 ASN Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [389, 382, 310, 89, 51, 160, 345, 408, 359, 40, 384] chunk 389 optimal weight: 5.9990 chunk 382 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 408 optimal weight: 0.0030 chunk 359 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 384 optimal weight: 0.5980 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN G 142 ASN E 140 GLN D 89 GLN W 43 GLN U 43 GLN U 142 ASN I 8 HIS T 593 ASN T 597 GLN X 142 ASN V 43 GLN V 142 ASN P 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.072155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.053647 restraints weight = 89159.664| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.73 r_work: 0.2538 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40098 Z= 0.143 Angle : 0.511 9.494 54591 Z= 0.259 Chirality : 0.043 0.154 5871 Planarity : 0.004 0.043 7266 Dihedral : 4.187 42.881 5570 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.37 % Allowed : 10.61 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.11), residues: 5040 helix: 0.78 (0.23), residues: 576 sheet: 0.40 (0.13), residues: 1686 loop : -0.26 (0.11), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 182 TYR 0.016 0.001 TYR Q 161 PHE 0.013 0.001 PHE A 632 TRP 0.011 0.001 TRP B 167 HIS 0.003 0.001 HIS I 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (40086) covalent geometry : angle 0.50049 / 0.26 (54555) hydrogen bonds : bond 0.03512 / 2.40 ( 880) hydrogen bonds : angle 5.24940 / 3.74 ( 2307) metal coordination : bond 0.00496 / 0.34 ( 12) metal coordination : angle 4.10330 / 2.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8956 (mt0) REVERT: H 75 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8488 (mtm-85) REVERT: H 162 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8579 (ttmm) REVERT: C 38 ASP cc_start: 0.8512 (m-30) cc_final: 0.7897 (m-30) REVERT: G 84 GLN cc_start: 0.8995 (mp10) cc_final: 0.8781 (mp10) REVERT: G 129 GLU cc_start: 0.7650 (pp20) cc_final: 0.7188 (pp20) REVERT: A 609 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: D 82 GLU cc_start: 0.8906 (mp0) cc_final: 0.8313 (mp0) REVERT: S 597 GLN cc_start: 0.8130 (mt0) cc_final: 0.7853 (tt0) REVERT: S 610 ASN cc_start: 0.8889 (m110) cc_final: 0.8400 (m-40) REVERT: W 70 ILE cc_start: 0.8612 (mm) cc_final: 0.8393 (pt) REVERT: W 88 LYS cc_start: 0.8865 (tptm) cc_final: 0.8628 (tmmt) REVERT: W 123 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6186 (ptp-170) REVERT: W 129 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: W 158 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7761 (tmtp) REVERT: W 162 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8527 (ttmt) REVERT: M 38 ASP cc_start: 0.8799 (m-30) cc_final: 0.8322 (m-30) REVERT: U 88 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8466 (mtpp) REVERT: U 117 PHE cc_start: 0.8417 (m-80) cc_final: 0.7998 (m-80) REVERT: U 129 GLU cc_start: 0.7894 (pp20) cc_final: 0.7291 (pp20) REVERT: I 180 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8125 (pp20) REVERT: I 190 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8416 (ttm110) REVERT: I 584 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8861 (t0) REVERT: I 609 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: O 82 GLU cc_start: 0.8747 (mp0) cc_final: 0.8290 (mp0) REVERT: K 159 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8078 (mtp180) REVERT: T 610 ASN cc_start: 0.8635 (m-40) cc_final: 0.8168 (m-40) REVERT: X 70 ILE cc_start: 0.8568 (mm) cc_final: 0.8209 (pt) REVERT: X 129 GLU cc_start: 0.8087 (tt0) cc_final: 0.7594 (tm-30) REVERT: V 117 PHE cc_start: 0.8401 (m-80) cc_final: 0.8023 (m-80) REVERT: V 129 GLU cc_start: 0.7767 (pp20) cc_final: 0.7301 (pp20) REVERT: V 158 LYS cc_start: 0.7527 (tmmm) cc_final: 0.7208 (tmmt) REVERT: J 246 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7917 (mtm-85) REVERT: J 584 ASP cc_start: 0.9223 (OUTLIER) cc_final: 0.8945 (t0) REVERT: J 609 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: P 82 GLU cc_start: 0.8820 (mp0) cc_final: 0.8401 (mp0) REVERT: L 167 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8436 (m100) outliers start: 56 outliers final: 20 residues processed: 370 average time/residue: 0.9805 time to fit residues: 419.2625 Evaluate side-chains 341 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 167 TRP Chi-restraints excluded: chain W residue 123 ARG Chi-restraints excluded: chain W residue 129 GLU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 614 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 246 ARG Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 393 ASN Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 609 GLU Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [399, 179, 100, 136, 338, 343, 221, 90, 481, 77, 259] chunk 399 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 338 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 221 optimal weight: 0.0010 chunk 90 optimal weight: 1.9990 chunk 481 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 597 GLN G 43 GLN G 142 ASN E 140 GLN A 8 HIS D 89 GLN B 220 HIS W 43 GLN U 43 GLN U 65 GLN U 142 ASN O 25 GLN O 112 ASN T 593 ASN T 597 GLN X 43 GLN V 43 GLN V 142 ASN P 89 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.054545 restraints weight = 88700.001| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.72 r_work: 0.2559 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40098 Z= 0.099 Angle : 0.482 8.610 54591 Z= 0.244 Chirality : 0.042 0.151 5871 Planarity : 0.004 0.042 7266 Dihedral : 3.993 43.025 5570 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.27 % Allowed : 11.05 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 5040 helix: 0.86 (0.23), residues: 576 sheet: 0.47 (0.13), residues: 1671 loop : -0.20 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 182 TYR 0.014 0.001 TYR Q 161 PHE 0.013 0.001 PHE A 632 TRP 0.011 0.001 TRP J 283 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (40086) covalent geometry : angle 0.47325 / 0.24 (54555) hydrogen bonds : bond 0.03009 / 2.07 ( 880) hydrogen bonds : angle 5.03853 / 3.58 ( 2307) metal coordination : bond 0.00257 / 0.17 ( 12) metal coordination : angle 3.67542 / 2.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 597 GLN cc_start: 0.8096 (mt0) cc_final: 0.7885 (tt0) REVERT: H 43 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8866 (mt0) REVERT: H 75 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.8475 (mtm-85) REVERT: H 162 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (ttmm) REVERT: C 38 ASP cc_start: 0.8381 (m-30) cc_final: 0.7822 (m-30) REVERT: G 10 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8236 (mp) REVERT: G 84 GLN cc_start: 0.9032 (mp10) cc_final: 0.8782 (mp10) REVERT: G 88 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8422 (mmmm) REVERT: G 129 GLU cc_start: 0.7684 (pp20) cc_final: 0.7191 (pp20) REVERT: A 609 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: D 82 GLU cc_start: 0.8902 (mp0) cc_final: 0.8224 (mp0) REVERT: B 185 MET cc_start: 0.8957 (mtm) cc_final: 0.8701 (mtm) REVERT: S 597 GLN cc_start: 0.8154 (mt0) cc_final: 0.7898 (tt0) REVERT: S 610 ASN cc_start: 0.8887 (m110) cc_final: 0.8403 (m-40) REVERT: W 88 LYS cc_start: 0.9079 (tptm) cc_final: 0.8412 (tmmt) REVERT: W 158 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7811 (tmtp) REVERT: W 162 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8504 (ttmt) REVERT: M 38 ASP cc_start: 0.8770 (m-30) cc_final: 0.8305 (m-30) REVERT: U 88 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8477 (mtpp) REVERT: U 117 PHE cc_start: 0.8371 (m-80) cc_final: 0.8012 (m-80) REVERT: U 129 GLU cc_start: 0.7899 (pp20) cc_final: 0.7254 (pp20) REVERT: I 180 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8096 (pp20) REVERT: I 190 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (ttm110) REVERT: I 584 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8837 (t0) REVERT: I 609 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: I 756 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: O 82 GLU cc_start: 0.8717 (mp0) cc_final: 0.8362 (mp0) REVERT: K 185 MET cc_start: 0.9029 (mtp) cc_final: 0.8785 (mtm) REVERT: T 610 ASN cc_start: 0.8605 (m-40) cc_final: 0.8159 (m-40) REVERT: X 88 LYS cc_start: 0.8754 (tppp) cc_final: 0.8061 (tmmt) REVERT: X 129 GLU cc_start: 0.8036 (tt0) cc_final: 0.7552 (tm-30) REVERT: X 162 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8426 (ttmt) REVERT: V 117 PHE cc_start: 0.8377 (m-80) cc_final: 0.8010 (m-80) REVERT: V 129 GLU cc_start: 0.7760 (pp20) cc_final: 0.7224 (pp20) REVERT: V 158 LYS cc_start: 0.7416 (tmmm) cc_final: 0.7127 (tmmt) REVERT: J 246 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (mtp85) REVERT: J 584 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8979 (t70) REVERT: J 748 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.7814 (p0) REVERT: P 82 GLU cc_start: 0.8787 (mp0) cc_final: 0.8306 (mp0) REVERT: L 167 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8381 (m100) outliers start: 52 outliers final: 14 residues processed: 360 average time/residue: 0.9436 time to fit residues: 395.1739 Evaluate side-chains 322 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 167 TRP Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 614 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain X residue 84 GLN Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 246 ARG Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain J residue 748 ASP Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [206, 218, 228, 437, 246, 176, 241, 266, 115, 149, 377] chunk 206 optimal weight: 2.9990 chunk 218 optimal weight: 0.0770 chunk 228 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 377 optimal weight: 4.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN G 142 ASN E 140 GLN D 89 GLN D 112 ASN U 43 GLN U 65 GLN U 142 ASN Q 140 GLN O 25 GLN O 112 ASN T 593 ASN X 43 GLN X 142 ASN V 43 GLN V 142 ASN P 112 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.052553 restraints weight = 89724.334| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 2.71 r_work: 0.2518 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 40098 Z= 0.195 Angle : 0.544 10.133 54591 Z= 0.273 Chirality : 0.044 0.156 5871 Planarity : 0.004 0.046 7266 Dihedral : 4.165 42.044 5570 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.49 % Allowed : 11.69 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.11), residues: 5040 helix: 0.82 (0.23), residues: 576 sheet: 0.35 (0.13), residues: 1692 loop : -0.23 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 182 TYR 0.016 0.001 TYR Q 161 PHE 0.014 0.001 PHE H 83 TRP 0.012 0.001 TRP B 167 HIS 0.004 0.001 HIS K 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (40086) covalent geometry : angle 0.53063 / 0.27 (54555) hydrogen bonds : bond 0.03763 / 2.57 ( 880) hydrogen bonds : angle 5.13736 / 3.66 ( 2307) metal coordination : bond 0.00706 / 0.48 ( 12) metal coordination : angle 4.62539 / 3.14 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 1.513 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: H 43 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8868 (mt0) REVERT: H 49 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8748 (mp) REVERT: H 162 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8413 (ttmm) REVERT: C 10 ASP cc_start: 0.8496 (t0) cc_final: 0.8230 (t0) REVERT: C 38 ASP cc_start: 0.8519 (m-30) cc_final: 0.7915 (m-30) REVERT: G 88 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8391 (mtpp) REVERT: G 129 GLU cc_start: 0.7732 (pp20) cc_final: 0.7263 (pp20) REVERT: D 82 GLU cc_start: 0.8917 (mp0) cc_final: 0.8399 (mp0) REVERT: B 185 MET cc_start: 0.8940 (mtm) cc_final: 0.8627 (mtm) REVERT: S 610 ASN cc_start: 0.8933 (m110) cc_final: 0.8459 (m-40) REVERT: W 129 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: W 158 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7803 (tmtp) REVERT: M 38 ASP cc_start: 0.8778 (m-30) cc_final: 0.8296 (m-30) REVERT: U 117 PHE cc_start: 0.8377 (m-80) cc_final: 0.7940 (m-80) REVERT: U 129 GLU cc_start: 0.7976 (pp20) cc_final: 0.7443 (pp20) REVERT: I 180 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8107 (pp20) REVERT: I 190 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8458 (ttm110) REVERT: I 246 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7655 (mtm-85) REVERT: I 584 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8832 (t0) REVERT: O 82 GLU cc_start: 0.8791 (mp0) cc_final: 0.8265 (mp0) REVERT: K 159 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8283 (mtp180) REVERT: T 610 ASN cc_start: 0.8682 (m-40) cc_final: 0.8253 (m-40) REVERT: X 88 LYS cc_start: 0.8774 (tppp) cc_final: 0.8083 (tmmt) REVERT: X 129 GLU cc_start: 0.8134 (tt0) cc_final: 0.7602 (tm-30) REVERT: X 162 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8591 (ttmt) REVERT: V 117 PHE cc_start: 0.8407 (m-80) cc_final: 0.8012 (m-80) REVERT: V 129 GLU cc_start: 0.7780 (pp20) cc_final: 0.7210 (pp20) REVERT: V 158 LYS cc_start: 0.7430 (tmmm) cc_final: 0.7130 (tmmt) REVERT: J 246 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7881 (mtm-85) REVERT: J 584 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8973 (t70) REVERT: P 82 GLU cc_start: 0.8825 (mp0) cc_final: 0.8438 (mp0) REVERT: L 167 TRP cc_start: 0.9002 (OUTLIER) cc_final: 0.8519 (m100) outliers start: 61 outliers final: 30 residues processed: 349 average time/residue: 0.9660 time to fit residues: 390.2492 Evaluate side-chains 335 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 167 TRP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 57 LYS Chi-restraints excluded: chain W residue 129 GLU Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 246 ARG Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 614 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 246 ARG Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 609 GLU Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [352, 242, 157, 402, 83, 439, 125, 22, 19, 478, 305] chunk 352 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 402 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 439 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 478 optimal weight: 4.9990 chunk 305 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 597 GLN G 43 GLN G 142 ASN E 140 GLN D 112 ASN S 597 GLN U 43 GLN U 65 GLN O 112 ASN T 593 ASN X 43 GLN V 43 GLN V 142 ASN R 140 GLN P 112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.072114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.053778 restraints weight = 88990.793| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.72 r_work: 0.2545 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40098 Z= 0.110 Angle : 0.503 9.095 54591 Z= 0.254 Chirality : 0.042 0.170 5871 Planarity : 0.004 0.048 7266 Dihedral : 3.984 42.394 5570 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.05 % Allowed : 12.35 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 5040 helix: 0.74 (0.23), residues: 588 sheet: 0.44 (0.13), residues: 1677 loop : -0.18 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 182 TYR 0.014 0.001 TYR Q 161 PHE 0.013 0.001 PHE A 632 TRP 0.012 0.001 TRP A 283 HIS 0.003 0.001 HIS I 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (40086) covalent geometry : angle 0.49327 / 0.25 (54555) hydrogen bonds : bond 0.03074 / 2.11 ( 880) hydrogen bonds : angle 4.99820 / 3.56 ( 2307) metal coordination : bond 0.00297 / 0.20 ( 12) metal coordination : angle 3.87088 / 2.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 597 GLN cc_start: 0.8100 (mt0) cc_final: 0.7892 (tt0) REVERT: H 43 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8857 (mt0) REVERT: H 49 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8724 (mp) REVERT: H 162 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: C 10 ASP cc_start: 0.8520 (t0) cc_final: 0.8308 (t0) REVERT: C 38 ASP cc_start: 0.8465 (m-30) cc_final: 0.7878 (m-30) REVERT: G 10 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8258 (mp) REVERT: G 88 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8361 (mtpp) REVERT: G 129 GLU cc_start: 0.7781 (pp20) cc_final: 0.7295 (pp20) REVERT: A 609 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: D 82 GLU cc_start: 0.8920 (mp0) cc_final: 0.8356 (mp0) REVERT: B 185 MET cc_start: 0.8842 (mtm) cc_final: 0.8452 (mtm) REVERT: S 597 GLN cc_start: 0.8315 (tt0) cc_final: 0.8080 (tt0) REVERT: S 610 ASN cc_start: 0.8915 (m110) cc_final: 0.8387 (m110) REVERT: W 88 LYS cc_start: 0.9074 (tptm) cc_final: 0.8411 (ttpt) REVERT: W 158 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7899 (tmtp) REVERT: M 38 ASP cc_start: 0.8749 (m-30) cc_final: 0.8312 (m-30) REVERT: U 88 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8331 (mtpp) REVERT: U 117 PHE cc_start: 0.8306 (m-80) cc_final: 0.7825 (m-80) REVERT: U 129 GLU cc_start: 0.7992 (pp20) cc_final: 0.7470 (pp20) REVERT: I 190 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8542 (ttm110) REVERT: I 609 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: I 768 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8084 (tpp80) REVERT: O 82 GLU cc_start: 0.8779 (mp0) cc_final: 0.8391 (mp0) REVERT: T 610 ASN cc_start: 0.8665 (m-40) cc_final: 0.8261 (m-40) REVERT: X 88 LYS cc_start: 0.8728 (tppp) cc_final: 0.8039 (tmmt) REVERT: X 129 GLU cc_start: 0.8108 (tt0) cc_final: 0.7614 (tm-30) REVERT: X 158 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7777 (tmtp) REVERT: X 162 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8453 (ttmt) REVERT: V 45 GLU cc_start: 0.8996 (tt0) cc_final: 0.8379 (tp30) REVERT: V 117 PHE cc_start: 0.8248 (m-80) cc_final: 0.7903 (m-80) REVERT: V 129 GLU cc_start: 0.7781 (pp20) cc_final: 0.7195 (pp20) REVERT: V 158 LYS cc_start: 0.7446 (tmmm) cc_final: 0.7147 (tmmt) REVERT: J 609 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.7958 (tp30) REVERT: J 748 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.7855 (p0) REVERT: P 82 GLU cc_start: 0.8780 (mp0) cc_final: 0.8389 (mp0) REVERT: L 167 TRP cc_start: 0.8976 (OUTLIER) cc_final: 0.8503 (m100) outliers start: 43 outliers final: 21 residues processed: 354 average time/residue: 0.9528 time to fit residues: 392.1022 Evaluate side-chains 333 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 167 TRP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 614 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 393 ASN Chi-restraints excluded: chain J residue 609 GLU Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain J residue 748 ASP Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [355, 376, 304, 77, 165, 319, 173, 207, 137, 140, 63] chunk 355 optimal weight: 0.8980 chunk 376 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 173 optimal weight: 0.0010 chunk 207 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN G 142 ASN E 140 GLN U 43 GLN U 65 GLN U 142 ASN Q 140 GLN O 25 GLN T 593 ASN T 597 GLN X 43 GLN X 142 ASN V 43 GLN V 142 ASN P 112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.054177 restraints weight = 88592.435| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.71 r_work: 0.2559 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40098 Z= 0.101 Angle : 0.501 8.746 54591 Z= 0.253 Chirality : 0.042 0.192 5871 Planarity : 0.004 0.052 7266 Dihedral : 3.871 42.295 5570 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.00 % Allowed : 12.57 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 5040 helix: 0.78 (0.23), residues: 588 sheet: 0.42 (0.13), residues: 1728 loop : -0.09 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 182 TYR 0.016 0.001 TYR Q 161 PHE 0.012 0.001 PHE A 632 TRP 0.012 0.001 TRP A 283 HIS 0.002 0.001 HIS J 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (40086) covalent geometry : angle 0.49206 / 0.25 (54555) hydrogen bonds : bond 0.02925 / 2.01 ( 880) hydrogen bonds : angle 4.93551 / 3.51 ( 2307) metal coordination : bond 0.00260 / 0.17 ( 12) metal coordination : angle 3.77767 / 2.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 597 GLN cc_start: 0.8085 (mt0) cc_final: 0.7883 (tt0) REVERT: H 43 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8826 (mt0) REVERT: H 45 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7602 (tp30) REVERT: H 49 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8623 (mp) REVERT: H 162 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8435 (ttmm) REVERT: C 10 ASP cc_start: 0.8537 (t0) cc_final: 0.8336 (t0) REVERT: C 38 ASP cc_start: 0.8397 (m-30) cc_final: 0.7806 (m-30) REVERT: G 10 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8284 (mp) REVERT: G 88 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8320 (mtpp) REVERT: G 129 GLU cc_start: 0.7790 (pp20) cc_final: 0.7216 (pp20) REVERT: A 609 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: D 82 GLU cc_start: 0.8931 (mp0) cc_final: 0.8344 (mp0) REVERT: B 185 MET cc_start: 0.8753 (mtm) cc_final: 0.8346 (mtm) REVERT: S 597 GLN cc_start: 0.8322 (tt0) cc_final: 0.8076 (tt0) REVERT: S 610 ASN cc_start: 0.8865 (m110) cc_final: 0.8332 (m110) REVERT: W 129 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: W 158 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7925 (tmtp) REVERT: M 38 ASP cc_start: 0.8731 (m-30) cc_final: 0.8294 (m-30) REVERT: U 54 ARG cc_start: 0.8859 (mtp85) cc_final: 0.8572 (mtm-85) REVERT: U 88 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8277 (mtpp) REVERT: U 117 PHE cc_start: 0.8187 (m-80) cc_final: 0.7792 (m-80) REVERT: U 129 GLU cc_start: 0.7992 (pp20) cc_final: 0.7459 (pp20) REVERT: I 609 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: I 756 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: O 82 GLU cc_start: 0.8832 (mp0) cc_final: 0.8436 (mp0) REVERT: K 159 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8012 (mtp180) REVERT: T 610 ASN cc_start: 0.8635 (m-40) cc_final: 0.8220 (m-40) REVERT: X 88 LYS cc_start: 0.8735 (tppp) cc_final: 0.8053 (tmmt) REVERT: X 129 GLU cc_start: 0.8123 (tt0) cc_final: 0.7525 (tm-30) REVERT: X 158 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7771 (tmtp) REVERT: X 162 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8617 (ttmt) REVERT: V 45 GLU cc_start: 0.8973 (tt0) cc_final: 0.8411 (tp30) REVERT: V 117 PHE cc_start: 0.8202 (m-80) cc_final: 0.7867 (m-80) REVERT: V 129 GLU cc_start: 0.7770 (pp20) cc_final: 0.7170 (pp20) REVERT: V 158 LYS cc_start: 0.7412 (tmmm) cc_final: 0.7191 (tmmt) REVERT: J 180 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7632 (pp20) REVERT: J 609 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: J 748 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.7825 (p0) REVERT: P 82 GLU cc_start: 0.8811 (mp0) cc_final: 0.8393 (mp0) REVERT: L 167 TRP cc_start: 0.8953 (OUTLIER) cc_final: 0.8468 (m100) outliers start: 41 outliers final: 17 residues processed: 349 average time/residue: 0.9513 time to fit residues: 385.9077 Evaluate side-chains 329 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 129 GLU Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 614 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 756 GLN Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 609 GLU Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain J residue 748 ASP Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [418, 412, 420, 320, 442, 123, 53, 80, 220, 421, 367] chunk 418 optimal weight: 2.9990 chunk 412 optimal weight: 0.9980 chunk 420 optimal weight: 1.9990 chunk 320 optimal weight: 0.0470 chunk 442 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 220 optimal weight: 0.2980 chunk 421 optimal weight: 1.9990 chunk 367 optimal weight: 8.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN G 142 ASN E 140 GLN D 112 ASN U 43 GLN U 65 GLN Q 140 GLN T 593 ASN T 597 GLN X 43 GLN X 148 GLN V 43 GLN P 112 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.054323 restraints weight = 89223.454| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.71 r_work: 0.2562 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40098 Z= 0.103 Angle : 0.504 10.778 54591 Z= 0.253 Chirality : 0.042 0.172 5871 Planarity : 0.004 0.056 7266 Dihedral : 3.804 41.913 5570 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.90 % Allowed : 12.81 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.12), residues: 5040 helix: 0.79 (0.23), residues: 588 sheet: 0.44 (0.13), residues: 1728 loop : -0.05 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 182 TYR 0.015 0.001 TYR Q 161 PHE 0.012 0.001 PHE A 632 TRP 0.012 0.001 TRP A 283 HIS 0.002 0.001 HIS K 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 (40086) covalent geometry : angle 0.49486 / 0.25 (54555) hydrogen bonds : bond 0.02906 / 2.01 ( 880) hydrogen bonds : angle 4.89317 / 3.48 ( 2307) metal coordination : bond 0.00258 / 0.17 ( 12) metal coordination : angle 3.83660 / 2.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 597 GLN cc_start: 0.8097 (mt0) cc_final: 0.7850 (tt0) REVERT: H 43 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8885 (mt0) REVERT: H 49 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8646 (mp) REVERT: H 88 LYS cc_start: 0.8934 (tptp) cc_final: 0.8136 (tmmt) REVERT: H 162 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: C 10 ASP cc_start: 0.8570 (t0) cc_final: 0.8358 (t0) REVERT: G 58 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8853 (tttt) REVERT: G 88 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8322 (mtpp) REVERT: G 129 GLU cc_start: 0.7789 (pp20) cc_final: 0.7210 (pp20) REVERT: A 609 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: D 82 GLU cc_start: 0.8946 (mp0) cc_final: 0.8403 (mp0) REVERT: B 185 MET cc_start: 0.8744 (mtm) cc_final: 0.8300 (mtm) REVERT: S 597 GLN cc_start: 0.8383 (tt0) cc_final: 0.8151 (tt0) REVERT: S 610 ASN cc_start: 0.8974 (m110) cc_final: 0.8462 (m110) REVERT: W 123 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6067 (ptp-170) REVERT: W 129 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: M 38 ASP cc_start: 0.8739 (m-30) cc_final: 0.8250 (m-30) REVERT: U 88 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8351 (mtpp) REVERT: U 117 PHE cc_start: 0.8143 (m-80) cc_final: 0.7775 (m-80) REVERT: U 129 GLU cc_start: 0.8000 (pp20) cc_final: 0.7481 (pp20) REVERT: I 532 LYS cc_start: 0.8454 (ptmm) cc_final: 0.8197 (mtmm) REVERT: I 609 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: I 768 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8039 (tpp80) REVERT: O 82 GLU cc_start: 0.8838 (mp0) cc_final: 0.8435 (mp0) REVERT: K 159 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7975 (mtp180) REVERT: T 610 ASN cc_start: 0.8720 (m-40) cc_final: 0.8296 (m-40) REVERT: X 88 LYS cc_start: 0.8706 (tppp) cc_final: 0.8044 (tmmt) REVERT: X 129 GLU cc_start: 0.8179 (tt0) cc_final: 0.7550 (tm-30) REVERT: X 158 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7749 (tmtp) REVERT: X 162 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8621 (ttmt) REVERT: V 117 PHE cc_start: 0.8138 (m-80) cc_final: 0.7831 (m-80) REVERT: V 129 GLU cc_start: 0.7797 (pp20) cc_final: 0.7188 (pp20) REVERT: J 180 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7677 (pp20) REVERT: J 583 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8065 (tt0) REVERT: J 609 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: J 748 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.7788 (p0) REVERT: P 82 GLU cc_start: 0.8834 (mp0) cc_final: 0.8408 (mp0) REVERT: L 167 TRP cc_start: 0.8946 (OUTLIER) cc_final: 0.8498 (m100) outliers start: 37 outliers final: 14 residues processed: 343 average time/residue: 0.9414 time to fit residues: 375.5706 Evaluate side-chains 326 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 123 ARG Chi-restraints excluded: chain W residue 129 GLU Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 609 GLU Chi-restraints excluded: chain J residue 748 ASP Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [294, 119, 214, 94, 93, 51, 291, 440, 441, 192, 73] chunk 294 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 440 optimal weight: 0.5980 chunk 441 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN G 142 ASN E 140 GLN D 112 ASN U 43 GLN U 65 GLN Q 140 GLN O 25 GLN X 43 GLN X 142 ASN V 43 GLN P 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.054393 restraints weight = 88510.553| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.71 r_work: 0.2564 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40098 Z= 0.107 Angle : 0.523 12.887 54591 Z= 0.262 Chirality : 0.042 0.171 5871 Planarity : 0.004 0.082 7266 Dihedral : 3.787 41.627 5570 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.76 % Allowed : 13.06 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 5040 helix: 0.76 (0.23), residues: 588 sheet: 0.45 (0.13), residues: 1728 loop : -0.03 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG J 790 TYR 0.016 0.001 TYR Q 161 PHE 0.012 0.001 PHE A 632 TRP 0.012 0.001 TRP A 283 HIS 0.003 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (40086) covalent geometry : angle 0.51313 / 0.26 (54555) hydrogen bonds : bond 0.02966 / 2.07 ( 880) hydrogen bonds : angle 4.93081 / 3.51 ( 2307) metal coordination : bond 0.00274 / 0.18 ( 12) metal coordination : angle 3.89153 / 2.58 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 597 GLN cc_start: 0.8108 (mt0) cc_final: 0.7846 (tt0) REVERT: H 43 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8867 (mt0) REVERT: H 49 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8622 (mp) REVERT: H 88 LYS cc_start: 0.8973 (tptp) cc_final: 0.8244 (tmmt) REVERT: H 158 LYS cc_start: 0.7883 (tptp) cc_final: 0.7617 (tptp) REVERT: H 162 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8436 (ttmm) REVERT: C 10 ASP cc_start: 0.8586 (t0) cc_final: 0.8368 (t0) REVERT: G 129 GLU cc_start: 0.7788 (pp20) cc_final: 0.7208 (pp20) REVERT: A 609 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: D 82 GLU cc_start: 0.8952 (mp0) cc_final: 0.8398 (mp0) REVERT: B 185 MET cc_start: 0.8736 (mtm) cc_final: 0.8292 (mtm) REVERT: S 597 GLN cc_start: 0.8318 (tt0) cc_final: 0.8099 (tt0) REVERT: S 610 ASN cc_start: 0.8956 (m110) cc_final: 0.8449 (m110) REVERT: W 123 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6029 (ptp-170) REVERT: W 129 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: M 38 ASP cc_start: 0.8691 (m-30) cc_final: 0.8230 (m-30) REVERT: U 88 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8445 (mtpp) REVERT: U 117 PHE cc_start: 0.8126 (m-80) cc_final: 0.7755 (m-80) REVERT: U 129 GLU cc_start: 0.7971 (pp20) cc_final: 0.7440 (pp20) REVERT: I 532 LYS cc_start: 0.8456 (ptmm) cc_final: 0.8211 (mtmm) REVERT: I 609 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: I 768 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8004 (mpp-170) REVERT: O 82 GLU cc_start: 0.8842 (mp0) cc_final: 0.8436 (mp0) REVERT: K 159 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8034 (mtp180) REVERT: T 610 ASN cc_start: 0.8710 (m-40) cc_final: 0.8314 (m-40) REVERT: X 88 LYS cc_start: 0.8758 (tppp) cc_final: 0.8047 (tmmt) REVERT: X 129 GLU cc_start: 0.8151 (tt0) cc_final: 0.7551 (tm-30) REVERT: X 158 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7744 (tmtp) REVERT: X 162 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8623 (ttmt) REVERT: V 45 GLU cc_start: 0.8925 (tt0) cc_final: 0.8413 (tp30) REVERT: V 117 PHE cc_start: 0.8121 (m-80) cc_final: 0.7816 (m-80) REVERT: V 129 GLU cc_start: 0.7782 (pp20) cc_final: 0.7178 (pp20) REVERT: J 583 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8057 (tt0) REVERT: J 609 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: J 748 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7786 (p0) REVERT: P 82 GLU cc_start: 0.8796 (mp0) cc_final: 0.8396 (mp0) REVERT: L 167 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8496 (m100) outliers start: 31 outliers final: 16 residues processed: 330 average time/residue: 0.9427 time to fit residues: 361.5719 Evaluate side-chains 327 residues out of total 4089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 123 ARG Chi-restraints excluded: chain W residue 129 GLU Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 609 GLU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain K residue 159 ARG Chi-restraints excluded: chain K residue 167 TRP Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 370 MET Chi-restraints excluded: chain J residue 609 GLU Chi-restraints excluded: chain J residue 748 ASP Chi-restraints excluded: chain L residue 167 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: [459, 121, 383, 266, 431, 221, 291, 153, 488, 242, 296] chunk 459 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 383 optimal weight: 0.6980 chunk 266 optimal weight: 0.7980 chunk 431 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 488 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN E 140 GLN U 43 GLN U 65 GLN O 25 GLN T 597 GLN X 43 GLN X 148 GLN V 43 GLN P 112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.054303 restraints weight = 89288.972| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.72 r_work: 0.2561 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40098 Z= 0.111 Angle : 0.529 14.682 54591 Z= 0.265 Chirality : 0.042 0.193 5871 Planarity : 0.004 0.066 7266 Dihedral : 3.781 41.256 5570 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.78 % Allowed : 13.06 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 5040 helix: 0.74 (0.23), residues: 588 sheet: 0.45 (0.13), residues: 1758 loop : -0.00 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 182 TYR 0.016 0.001 TYR Q 161 PHE 0.012 0.001 PHE A 632 TRP 0.011 0.001 TRP A 283 HIS 0.002 0.001 HIS K 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (40086) covalent geometry : angle 0.51899 / 0.27 (54555) hydrogen bonds : bond 0.03039 / 2.12 ( 880) hydrogen bonds : angle 4.95054 / 3.53 ( 2307) metal coordination : bond 0.00298 / 0.20 ( 12) metal coordination : angle 3.93227 / 2.61 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12972.11 seconds wall clock time: 220 minutes 52.93 seconds (13252.93 seconds total)