Starting phenix.real_space_refine on Fri Jan 16 12:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p7e_13236/01_2026/7p7e_13236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7e_13236/01_2026/7p7e_13236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p7e_13236/01_2026/7p7e_13236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7e_13236/01_2026/7p7e_13236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p7e_13236/01_2026/7p7e_13236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7e_13236/01_2026/7p7e_13236.map" } resolution = 2.7 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= 0.005 sd= 0.022 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 10 5.49 5 S 264 5.16 5 C 23766 2.51 5 N 6010 2.21 5 O 7243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37326 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4571 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 530} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1320 Classifications: {'peptide': 166} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 154} Chain breaks: 3 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2330 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 283} Chain breaks: 2 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4508 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 573} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1203 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 367 Classifications: {'water': 367} Link IDs: {None: 366} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "M" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 81.895 55.434 191.821 1.00 9.21 S ATOM 2766 SG CYS F 357 85.579 55.023 196.013 1.00 12.11 S ATOM 3087 SG CYS F 398 80.201 51.064 196.582 1.00 18.40 S ATOM 2722 SG CYS F 351 84.613 49.245 192.558 1.00 9.65 S ATOM 4079 SG CYS E 92 94.729 46.915 211.595 1.00 36.85 S ATOM 4113 SG CYS E 97 95.069 47.410 215.097 1.00 33.34 S ATOM 4391 SG CYS E 133 89.585 45.769 211.558 1.00 27.78 S ATOM 4417 SG CYS E 137 88.962 46.257 214.880 1.00 38.87 S ATOM 5501 SG CYS G 114 90.606 63.602 174.094 1.00 14.25 S ATOM 5441 SG CYS G 105 95.542 67.842 175.545 1.00 13.84 S ATOM 5461 SG CYS G 108 96.710 62.038 172.974 1.00 15.90 S ATOM 5855 SG CYS G 156 85.954 54.975 178.884 1.00 16.70 S ATOM 5836 SG CYS G 153 92.043 54.233 181.492 1.00 19.12 S ATOM 5884 SG CYS G 159 89.408 49.600 177.824 1.00 10.89 S ATOM 6228 SG CYS G 203 90.850 55.166 174.958 1.00 10.87 S ATOM 6453 SG CYS G 230 86.941 47.614 153.562 1.00 15.17 S ATOM 6738 SG CYS G 265 87.571 43.521 158.654 1.00 18.20 S ATOM 6501 SG CYS G 237 81.895 46.610 157.020 1.00 7.20 S ATOM 6477 SG CYS G 233 84.361 41.649 153.456 1.00 14.58 S ATOM 4902 SG CYS G 36 79.630 55.021 182.081 1.00 17.75 S ATOM 4978 SG CYS G 47 80.948 58.536 182.548 1.00 16.12 S ATOM 5004 SG CYS G 50 75.047 59.600 182.936 1.00 11.76 S ATOM 5153 SG CYS G 69 74.827 56.037 182.328 1.00 12.48 S ATOM 16854 SG CYS B 129 96.888 93.226 151.405 1.00 25.43 S ATOM 16490 SG CYS B 64 101.672 97.519 152.939 1.00 54.49 S ATOM 16484 SG CYS B 63 95.828 98.368 155.424 1.00 46.87 S ATOM 17071 SG CYS B 158 99.276 92.994 157.071 1.00 40.22 S ATOM 18104 SG CYS I 102 98.570 86.666 162.812 1.00 13.24 S ATOM 18079 SG CYS I 99 103.919 86.037 158.805 1.00 15.22 S ATOM 18122 SG CYS I 105 103.162 82.340 164.036 1.00 21.87 S ATOM 17837 SG CYS I 70 98.985 81.609 159.071 1.00 9.60 S ATOM 18151 SG CYS I 109 105.056 76.628 169.907 1.00 15.42 S ATOM 17814 SG CYS I 66 102.751 76.060 163.902 1.00 16.32 S ATOM 17774 SG CYS I 60 107.435 72.053 165.673 1.00 11.86 S ATOM 17792 SG CYS I 63 101.317 71.826 168.571 1.00 8.61 S Time building chain proxies: 8.52, per 1000 atoms: 0.23 Number of scatterers: 37326 At special positions: 0 Unit cell: (157.5, 215.5, 246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 264 16.00 P 10 15.00 O 7243 8.00 N 6010 7.00 C 23766 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: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8430 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 0 sheets defined 52.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.856A pdb=" N ASP F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 302 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.619A pdb=" N SER E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.842A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 276 removed outlier: 5.127A pdb=" N TYR G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR G 274 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.436A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.510A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 605 removed outlier: 4.840A pdb=" N ASN G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 605' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 5.343A pdb=" N GLY G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE G 688 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS G 689 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP G 690 " --> pdb=" O ALA G 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 683 through 690' Processing helix chain 'G' and resid 764 through 768 removed outlier: 5.128A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 768' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 4.995A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 5.519A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 63 through 68 removed outlier: 4.267A pdb=" N GLU B 67 " --> pdb=" O CYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'H' and resid 6 through 37 Processing helix chain 'H' and resid 56 through 69 removed outlier: 4.634A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 5.020A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 4.366A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.879A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 231 through 257 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'L' and resid 4 through 20 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.372A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 560 removed outlier: 5.261A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 49 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 233 Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 256 through 262 Processing helix chain 'M' and resid 266 through 275 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 501 removed outlier: 4.931A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.415A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 320 through 347 removed outlier: 5.340A pdb=" N GLU N 324 " --> pdb=" O GLU N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.895A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1662 hydrogen bonds defined for protein. 4986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15501 1.42 - 1.64: 21394 1.64 - 1.86: 402 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37389 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.373 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.607 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.80e+00 ... (remaining 37384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 50040 2.73 - 5.46: 517 5.46 - 8.19: 122 8.19 - 10.92: 17 10.92 - 13.65: 10 Bond angle restraints: 50706 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.07 12.74 2.21e+00 2.05e-01 3.33e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 134.02 -12.22 2.44e+00 1.68e-01 2.51e+01 angle pdb=" CB LYS E 116 " pdb=" CG LYS E 116 " pdb=" CD LYS E 116 " ideal model delta sigma weight residual 111.30 122.71 -11.41 2.30e+00 1.89e-01 2.46e+01 angle pdb=" CA ILE N 135 " pdb=" CB ILE N 135 " pdb=" CG1 ILE N 135 " ideal model delta sigma weight residual 110.40 118.69 -8.29 1.70e+00 3.46e-01 2.38e+01 angle pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 ... (remaining 50701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 20102 22.30 - 44.60: 1565 44.60 - 66.91: 304 66.91 - 89.21: 43 89.21 - 111.51: 9 Dihedral angle restraints: 22023 sinusoidal: 8851 harmonic: 13172 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.35 34.65 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA TRP G 668 " pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta harmonic sigma weight residual 180.00 146.03 33.97 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 22020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.241: 5642 4.241 - 8.483: 0 8.483 - 12.724: 0 12.724 - 16.966: 0 16.966 - 21.207: 28 Chirality restraints: 5670 Sorted by residual: chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.65 21.21 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5667 not shown) Planarity restraints: 6330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO N 65 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL N 63 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.019 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 48 " 0.015 2.00e-02 2.50e+03 1.79e-02 8.03e+00 pdb=" CG TRP B 48 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 48 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 48 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 48 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 48 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 48 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 48 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 48 " -0.001 2.00e-02 2.50e+03 ... (remaining 6327 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1735 2.72 - 3.26: 36927 3.26 - 3.81: 69706 3.81 - 4.35: 89107 4.35 - 4.90: 142362 Nonbonded interactions: 339837 Sorted by model distance: nonbonded pdb=" O GLY L 421 " pdb=" OG1 THR L 425 " model vdw 2.170 3.040 nonbonded pdb=" O HOH G1123 " pdb=" O HOH G1305 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLN E 103 " pdb=" O HOH E 301 " model vdw 2.248 3.040 nonbonded pdb=" O HOH G1107 " pdb=" O HOH G1379 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.249 3.040 ... (remaining 339832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 3.470 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 39.350 Find NCS groups from input model: 0.440 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:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.005 0.157 37425 Z= 0.225 Angle : 0.802 13.648 50799 Z= 0.401 Chirality : 1.486 21.207 5670 Planarity : 0.006 0.077 6330 Dihedral : 16.277 111.512 13593 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 1.94 % Allowed : 18.31 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4558 helix: 0.39 (0.09), residues: 2634 sheet: -0.45 (0.29), residues: 306 loop : -0.76 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 562 TYR 0.028 0.002 TYR N 260 PHE 0.041 0.002 PHE L 341 TRP 0.049 0.002 TRP B 48 HIS 0.019 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.00480 (37389) covalent geometry : angle 0.78447 (50706) hydrogen bonds : bond 0.06235 ( 1662) hydrogen bonds : angle 4.91424 ( 4986) metal coordination : bond 0.05692 ( 36) metal coordination : angle 3.93332 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 520 time to evaluate : 1.477 Fit side-chains REVERT: F 373 ARG cc_start: 0.8639 (mtp180) cc_final: 0.8425 (mtp180) REVERT: E 156 GLU cc_start: 0.8871 (pm20) cc_final: 0.8605 (mp0) REVERT: G 904 ASP cc_start: 0.8335 (m-30) cc_final: 0.8039 (t0) REVERT: C 216 MET cc_start: 0.4548 (ttm) cc_final: 0.3923 (tmm) REVERT: C 340 PHE cc_start: 0.8238 (t80) cc_final: 0.7527 (t80) REVERT: H 238 PHE cc_start: 0.8206 (m-80) cc_final: 0.7827 (m-80) REVERT: L 407 MET cc_start: 0.6393 (mmt) cc_final: 0.5198 (tmm) REVERT: M 304 MET cc_start: 0.8618 (mmm) cc_final: 0.8343 (mmm) REVERT: N 8 LEU cc_start: 0.6822 (tm) cc_final: 0.6587 (mm) REVERT: N 447 ASN cc_start: 0.7748 (m110) cc_final: 0.7538 (m110) REVERT: N 480 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6548 (pp) outliers start: 73 outliers final: 47 residues processed: 580 average time/residue: 0.7018 time to fit residues: 490.5632 Evaluate side-chains 528 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 480 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 497 SER Chi-restraints excluded: chain L residue 612 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 455 GLN Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 254 VAL Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain J residue 24 ASN Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN E 78 GLN E 82 GLN G 299 GLN G 513 GLN G 583 ASN G 765 GLN G 768 ASN G 845 ASN G 901 HIS C 359 HIS B 173 GLN B 198 GLN B 213 ASN H 183 GLN H 312 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 435 HIS K 5 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074716 restraints weight = 43964.218| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.27 r_work: 0.2904 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.254 37425 Z= 0.412 Angle : 2.525 50.844 50799 Z= 1.453 Chirality : 0.453 6.543 5670 Planarity : 0.005 0.067 6330 Dihedral : 9.322 114.657 5526 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 3.27 % Allowed : 16.10 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.58 (0.12), residues: 4558 helix: 1.05 (0.10), residues: 2638 sheet: -0.19 (0.29), residues: 306 loop : -0.49 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 562 TYR 0.025 0.002 TYR N 260 PHE 0.034 0.002 PHE H 277 TRP 0.021 0.001 TRP B 48 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01175 (37389) covalent geometry : angle 2.20722 (50706) hydrogen bonds : bond 0.05958 ( 1662) hydrogen bonds : angle 4.51546 ( 4986) metal coordination : bond 0.05740 ( 36) metal coordination : angle 28.75044 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 506 time to evaluate : 1.640 Fit side-chains REVERT: E 116 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8847 (mmpt) REVERT: E 163 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: G 252 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: G 586 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8475 (mp) REVERT: G 750 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8517 (ppt-90) REVERT: G 852 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8086 (mp) REVERT: G 890 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.4805 (mpt) REVERT: C 216 MET cc_start: 0.4675 (ttm) cc_final: 0.3996 (tmm) REVERT: C 340 PHE cc_start: 0.7693 (t80) cc_final: 0.7404 (t80) REVERT: H 68 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7727 (t80) REVERT: H 238 PHE cc_start: 0.7827 (m-80) cc_final: 0.7586 (t80) REVERT: L 407 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5175 (tmm) REVERT: M 323 MET cc_start: 0.8689 (mmp) cc_final: 0.8369 (mmm) REVERT: M 407 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: N 480 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6796 (pp) REVERT: K 5 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8232 (mt0) outliers start: 123 outliers final: 44 residues processed: 574 average time/residue: 0.7016 time to fit residues: 487.6426 Evaluate side-chains 535 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 480 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 396 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 319 optimal weight: 0.0270 chunk 132 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN G 583 ASN G 749 HIS C 101 HIS C 283 ASN B 173 GLN B 198 GLN B 213 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS K 5 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.076684 restraints weight = 43916.592| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.26 r_work: 0.2947 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 37425 Z= 0.391 Angle : 2.516 50.635 50799 Z= 1.450 Chirality : 0.448 6.491 5670 Planarity : 0.004 0.067 6330 Dihedral : 8.925 113.132 5491 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 2.76 % Allowed : 16.82 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.96 (0.12), residues: 4558 helix: 1.41 (0.10), residues: 2637 sheet: -0.18 (0.30), residues: 302 loop : -0.38 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 859 TYR 0.022 0.001 TYR M 435 PHE 0.031 0.001 PHE N 72 TRP 0.020 0.001 TRP B 48 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01142 (37389) covalent geometry : angle 2.19580 (50706) hydrogen bonds : bond 0.05023 ( 1662) hydrogen bonds : angle 4.29278 ( 4986) metal coordination : bond 0.03746 ( 36) metal coordination : angle 28.81241 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 506 time to evaluate : 1.430 Fit side-chains REVERT: E 103 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: E 116 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8879 (mmpt) REVERT: E 163 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: G 586 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8543 (mp) REVERT: G 852 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8074 (mp) REVERT: C 216 MET cc_start: 0.4690 (ttm) cc_final: 0.3985 (tmm) REVERT: C 340 PHE cc_start: 0.7644 (t80) cc_final: 0.7368 (t80) REVERT: H 68 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7709 (t80) REVERT: L 407 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.4935 (ttp) REVERT: M 323 MET cc_start: 0.8532 (mmp) cc_final: 0.8230 (mmm) REVERT: M 407 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: N 480 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6792 (pp) outliers start: 104 outliers final: 43 residues processed: 572 average time/residue: 0.6904 time to fit residues: 477.5076 Evaluate side-chains 527 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 476 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 111 ILE Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 454 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 145 optimal weight: 0.0470 chunk 130 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 113 ASN G 583 ASN B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.074599 restraints weight = 43743.084| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.25 r_work: 0.2901 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37425 Z= 0.404 Angle : 2.521 50.547 50799 Z= 1.452 Chirality : 0.452 6.573 5670 Planarity : 0.004 0.064 6330 Dihedral : 9.019 114.223 5484 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 3.51 % Allowed : 16.40 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4558 helix: 1.38 (0.10), residues: 2654 sheet: -0.14 (0.30), residues: 306 loop : -0.29 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 86 TYR 0.021 0.002 TYR L 428 PHE 0.034 0.002 PHE H 277 TRP 0.021 0.001 TRP B 48 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01162 (37389) covalent geometry : angle 2.20402 (50706) hydrogen bonds : bond 0.05761 ( 1662) hydrogen bonds : angle 4.41178 ( 4986) metal coordination : bond 0.04508 ( 36) metal coordination : angle 28.69157 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 499 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: E 103 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: E 116 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8901 (mmpt) REVERT: E 163 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: G 252 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: G 586 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8527 (mp) REVERT: G 750 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8553 (ppt-90) REVERT: G 852 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8094 (mp) REVERT: G 890 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.4899 (mpt) REVERT: C 216 MET cc_start: 0.4920 (ttm) cc_final: 0.4191 (tmm) REVERT: C 340 PHE cc_start: 0.7638 (t80) cc_final: 0.7400 (t80) REVERT: B 65 TYR cc_start: 0.7359 (t80) cc_final: 0.6956 (t80) REVERT: I 83 LYS cc_start: 0.8221 (mppt) cc_final: 0.7979 (mmmt) REVERT: H 68 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7740 (t80) REVERT: H 238 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: L 407 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.4828 (tmm) REVERT: M 165 LYS cc_start: 0.8025 (tttm) cc_final: 0.7792 (tptp) REVERT: M 323 MET cc_start: 0.8666 (mmp) cc_final: 0.8375 (mmm) REVERT: M 407 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: N 8 LEU cc_start: 0.6934 (tm) cc_final: 0.6494 (mt) REVERT: N 480 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6816 (pp) outliers start: 132 outliers final: 57 residues processed: 577 average time/residue: 0.6919 time to fit residues: 482.9537 Evaluate side-chains 553 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 111 ILE Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 125 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 430 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 339 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 196 ASN F 224 ASN F 237 GLN G 232 GLN G 583 ASN B 173 GLN B 198 GLN H 226 HIS ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 451 GLN N 46 ASN N 123 ASN N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071867 restraints weight = 43799.702| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.27 r_work: 0.2842 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.240 37425 Z= 0.452 Angle : 2.543 50.536 50799 Z= 1.462 Chirality : 0.457 6.693 5670 Planarity : 0.005 0.057 6330 Dihedral : 9.682 115.262 5484 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.93 % Allowed : 15.87 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.70 (0.12), residues: 4558 helix: 1.12 (0.10), residues: 2653 sheet: -0.29 (0.29), residues: 311 loop : -0.37 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 86 TYR 0.022 0.002 TYR L 428 PHE 0.040 0.002 PHE H 277 TRP 0.023 0.002 TRP G 668 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01246 (37389) covalent geometry : angle 2.22925 (50706) hydrogen bonds : bond 0.07230 ( 1662) hydrogen bonds : angle 4.76583 ( 4986) metal coordination : bond 0.05679 ( 36) metal coordination : angle 28.66778 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 498 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: E 116 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8902 (mmpt) REVERT: G 249 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8034 (mtt-85) REVERT: G 252 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: G 750 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8232 (ppt-90) REVERT: G 852 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8147 (mp) REVERT: G 890 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.4932 (mpt) REVERT: C 216 MET cc_start: 0.5121 (ttm) cc_final: 0.4384 (tmm) REVERT: B 52 ASN cc_start: 0.8524 (m-40) cc_final: 0.8296 (m-40) REVERT: H 68 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7764 (t80) REVERT: H 238 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: A 67 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8079 (mmtt) REVERT: L 379 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8192 (t80) REVERT: L 407 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.4912 (tmm) REVERT: M 64 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: M 165 LYS cc_start: 0.8141 (tttm) cc_final: 0.7921 (tptp) REVERT: M 382 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8252 (mtmm) REVERT: N 376 MET cc_start: 0.7242 (tpp) cc_final: 0.6708 (tpp) REVERT: N 480 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6849 (pp) REVERT: J 86 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6685 (mp10) outliers start: 148 outliers final: 63 residues processed: 583 average time/residue: 0.6933 time to fit residues: 488.8597 Evaluate side-chains 558 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 482 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 382 LYS Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 347 optimal weight: 3.9990 chunk 321 optimal weight: 0.0970 chunk 452 optimal weight: 10.0000 chunk 444 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 583 ASN B 52 ASN B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 451 GLN N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075810 restraints weight = 42925.369| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.17 r_work: 0.2931 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 37425 Z= 0.391 Angle : 2.522 50.518 50799 Z= 1.452 Chirality : 0.448 6.492 5670 Planarity : 0.004 0.062 6330 Dihedral : 9.117 113.687 5482 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Rotamer: Outliers : 3.35 % Allowed : 16.69 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.12), residues: 4558 helix: 1.42 (0.10), residues: 2663 sheet: -0.16 (0.30), residues: 301 loop : -0.35 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 562 TYR 0.024 0.001 TYR M 435 PHE 0.032 0.001 PHE N 72 TRP 0.020 0.001 TRP G 668 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01142 (37389) covalent geometry : angle 2.20042 (50706) hydrogen bonds : bond 0.05279 ( 1662) hydrogen bonds : angle 4.39425 ( 4986) metal coordination : bond 0.03210 ( 36) metal coordination : angle 28.88159 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 504 time to evaluate : 3.195 Fit side-chains REVERT: E 116 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8904 (mmpt) REVERT: G 586 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8521 (mp) REVERT: G 845 ASN cc_start: 0.8907 (t0) cc_final: 0.8685 (t0) REVERT: G 852 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8095 (mp) REVERT: G 890 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.4686 (mpt) REVERT: C 206 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7186 (mtt) REVERT: C 216 MET cc_start: 0.5035 (ttm) cc_final: 0.4267 (tmm) REVERT: C 472 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: B 52 ASN cc_start: 0.8375 (m110) cc_final: 0.8159 (m-40) REVERT: H 63 ASP cc_start: 0.8528 (m-30) cc_final: 0.8324 (m-30) REVERT: H 68 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7735 (t80) REVERT: H 238 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: L 407 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.4899 (tmm) REVERT: L 430 PHE cc_start: 0.5775 (m-80) cc_final: 0.5456 (m-10) REVERT: M 165 LYS cc_start: 0.8063 (tttm) cc_final: 0.7847 (tptp) REVERT: M 323 MET cc_start: 0.8538 (mmp) cc_final: 0.8254 (mmm) REVERT: N 67 MET cc_start: 0.8182 (mtm) cc_final: 0.7748 (mtt) REVERT: N 376 MET cc_start: 0.7085 (tpp) cc_final: 0.6596 (tpp) REVERT: N 480 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6761 (pp) outliers start: 126 outliers final: 54 residues processed: 582 average time/residue: 0.6806 time to fit residues: 479.3647 Evaluate side-chains 550 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 487 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 346 optimal weight: 7.9990 chunk 290 optimal weight: 4.9990 chunk 444 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 422 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 364 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 583 ASN C 283 ASN B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.074101 restraints weight = 43120.299| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.18 r_work: 0.2894 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37425 Z= 0.408 Angle : 2.527 50.647 50799 Z= 1.455 Chirality : 0.452 6.571 5670 Planarity : 0.004 0.060 6330 Dihedral : 9.172 113.833 5482 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 3.19 % Allowed : 17.22 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4558 helix: 1.39 (0.10), residues: 2661 sheet: -0.16 (0.30), residues: 311 loop : -0.31 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 86 TYR 0.022 0.002 TYR L 428 PHE 0.033 0.002 PHE H 277 TRP 0.019 0.001 TRP G 668 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01168 (37389) covalent geometry : angle 2.20986 (50706) hydrogen bonds : bond 0.05938 ( 1662) hydrogen bonds : angle 4.48669 ( 4986) metal coordination : bond 0.04557 ( 36) metal coordination : angle 28.75024 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 498 time to evaluate : 1.454 Fit side-chains REVERT: E 116 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8902 (mmpt) REVERT: G 586 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8527 (mp) REVERT: G 845 ASN cc_start: 0.8932 (t0) cc_final: 0.8720 (t0) REVERT: G 852 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8112 (mp) REVERT: G 890 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.4915 (mpt) REVERT: C 216 MET cc_start: 0.5008 (ttm) cc_final: 0.4249 (tmm) REVERT: C 472 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: H 68 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7830 (t80) REVERT: H 238 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: L 379 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8021 (t80) REVERT: L 407 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.4944 (tmm) REVERT: L 430 PHE cc_start: 0.5872 (m-80) cc_final: 0.5500 (m-10) REVERT: M 64 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: M 165 LYS cc_start: 0.8082 (tttm) cc_final: 0.7874 (tptp) REVERT: M 323 MET cc_start: 0.8644 (mmp) cc_final: 0.8327 (mmm) REVERT: N 67 MET cc_start: 0.8201 (mtm) cc_final: 0.7748 (mtp) REVERT: N 323 MET cc_start: 0.7461 (ptp) cc_final: 0.6783 (ttm) REVERT: N 376 MET cc_start: 0.7152 (tpp) cc_final: 0.6632 (tpp) REVERT: N 480 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6778 (pp) outliers start: 120 outliers final: 66 residues processed: 568 average time/residue: 0.6913 time to fit residues: 475.4077 Evaluate side-chains 562 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 486 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 378 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 358 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 417 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 583 ASN B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073284 restraints weight = 42781.647| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.24 r_work: 0.2874 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37425 Z= 0.418 Angle : 2.533 50.603 50799 Z= 1.457 Chirality : 0.453 6.602 5670 Planarity : 0.004 0.058 6330 Dihedral : 9.327 112.850 5482 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 3.14 % Allowed : 17.35 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.90 (0.12), residues: 4558 helix: 1.30 (0.10), residues: 2659 sheet: -0.19 (0.30), residues: 303 loop : -0.33 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 562 TYR 0.022 0.002 TYR L 428 PHE 0.039 0.002 PHE H 277 TRP 0.022 0.001 TRP L 105 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01186 (37389) covalent geometry : angle 2.21707 (50706) hydrogen bonds : bond 0.06340 ( 1662) hydrogen bonds : angle 4.59042 ( 4986) metal coordination : bond 0.04886 ( 36) metal coordination : angle 28.73459 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 495 time to evaluate : 1.568 Fit side-chains REVERT: E 116 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8886 (mmpt) REVERT: G 252 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: G 750 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.8572 (ppt-90) REVERT: G 852 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8135 (mp) REVERT: G 890 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.4934 (mpt) REVERT: C 216 MET cc_start: 0.5066 (ttm) cc_final: 0.4448 (tmm) REVERT: C 472 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: H 68 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7850 (t80) REVERT: H 238 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 125 TRP cc_start: 0.7056 (m100) cc_final: 0.6459 (t-100) REVERT: L 168 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: M 64 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: M 165 LYS cc_start: 0.8103 (tttm) cc_final: 0.7899 (tptp) REVERT: M 323 MET cc_start: 0.8690 (mmp) cc_final: 0.8427 (mmm) REVERT: N 67 MET cc_start: 0.8219 (mtm) cc_final: 0.7759 (mtp) REVERT: N 323 MET cc_start: 0.7370 (ptp) cc_final: 0.6781 (ttm) REVERT: N 376 MET cc_start: 0.7152 (tpp) cc_final: 0.6641 (tpp) outliers start: 118 outliers final: 65 residues processed: 565 average time/residue: 0.7034 time to fit residues: 479.2574 Evaluate side-chains 560 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 486 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 122 TRP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 109 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 429 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 434 ASN G 583 ASN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073293 restraints weight = 42841.131| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.23 r_work: 0.2874 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 37425 Z= 0.419 Angle : 2.536 50.604 50799 Z= 1.458 Chirality : 0.453 6.598 5670 Planarity : 0.004 0.058 6330 Dihedral : 9.325 111.093 5479 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 2.84 % Allowed : 17.65 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.87 (0.12), residues: 4558 helix: 1.27 (0.10), residues: 2661 sheet: -0.19 (0.30), residues: 303 loop : -0.34 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 562 TYR 0.030 0.002 TYR N 260 PHE 0.042 0.002 PHE H 277 TRP 0.026 0.001 TRP L 105 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01187 (37389) covalent geometry : angle 2.21962 (50706) hydrogen bonds : bond 0.06336 ( 1662) hydrogen bonds : angle 4.61403 ( 4986) metal coordination : bond 0.04773 ( 36) metal coordination : angle 28.74264 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 491 time to evaluate : 1.588 Fit side-chains REVERT: E 116 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8809 (mmtt) REVERT: G 252 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: G 750 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.8568 (ppt-90) REVERT: G 852 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8134 (mp) REVERT: G 890 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.4942 (mpt) REVERT: C 216 MET cc_start: 0.5101 (ttm) cc_final: 0.4494 (tmm) REVERT: C 472 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: C 482 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8097 (tm-30) REVERT: H 68 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7858 (t80) REVERT: H 238 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 125 TRP cc_start: 0.7054 (m100) cc_final: 0.6487 (t-100) REVERT: L 430 PHE cc_start: 0.5912 (m-10) cc_final: 0.5459 (m-10) REVERT: M 64 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: M 323 MET cc_start: 0.8686 (mmp) cc_final: 0.8423 (mmm) REVERT: N 67 MET cc_start: 0.8252 (mtm) cc_final: 0.7829 (mtt) REVERT: N 323 MET cc_start: 0.7309 (ptp) cc_final: 0.6766 (ttm) REVERT: N 376 MET cc_start: 0.7144 (tpp) cc_final: 0.6637 (tpp) outliers start: 107 outliers final: 67 residues processed: 558 average time/residue: 0.7132 time to fit residues: 480.9028 Evaluate side-chains 554 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 479 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 626 GLU Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 454 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 122 TRP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 21 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 275 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 94 optimal weight: 0.0770 chunk 246 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 490 GLN G 583 ASN G 845 ASN B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076004 restraints weight = 42698.278| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.16 r_work: 0.2937 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37425 Z= 0.395 Angle : 2.528 50.593 50799 Z= 1.454 Chirality : 0.448 6.473 5670 Planarity : 0.004 0.062 6330 Dihedral : 8.901 107.169 5479 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 2.05 % Allowed : 18.50 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 4558 helix: 1.48 (0.10), residues: 2654 sheet: -0.09 (0.30), residues: 303 loop : -0.25 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 562 TYR 0.024 0.001 TYR M 435 PHE 0.038 0.001 PHE H 277 TRP 0.024 0.001 TRP L 105 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01150 (37389) covalent geometry : angle 2.20809 (50706) hydrogen bonds : bond 0.05237 ( 1662) hydrogen bonds : angle 4.39901 ( 4986) metal coordination : bond 0.03387 ( 36) metal coordination : angle 28.87288 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 501 time to evaluate : 1.497 Fit side-chains REVERT: E 116 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8828 (mmtt) REVERT: G 750 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8513 (ppt-90) REVERT: G 852 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8121 (mp) REVERT: G 890 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.4803 (mpt) REVERT: C 216 MET cc_start: 0.5021 (ttm) cc_final: 0.4472 (tmm) REVERT: C 482 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8057 (tm-30) REVERT: H 68 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7732 (t80) REVERT: H 183 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6545 (mt0) REVERT: H 238 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: A 125 TRP cc_start: 0.7004 (m100) cc_final: 0.6442 (t-100) REVERT: L 430 PHE cc_start: 0.5755 (m-10) cc_final: 0.5333 (m-10) REVERT: M 323 MET cc_start: 0.8541 (mmp) cc_final: 0.8260 (mmm) REVERT: N 67 MET cc_start: 0.8179 (mtm) cc_final: 0.7747 (mtt) REVERT: N 323 MET cc_start: 0.7235 (ptp) cc_final: 0.6727 (ttm) REVERT: N 376 MET cc_start: 0.7048 (tpp) cc_final: 0.6572 (tpp) outliers start: 77 outliers final: 56 residues processed: 550 average time/residue: 0.7144 time to fit residues: 473.5759 Evaluate side-chains 549 residues out of total 3771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 487 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 690 ASP Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 890 MET Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 CYS Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 183 GLN Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain M residue 122 TRP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 219 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 312 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 434 ASN G 490 GLN G 583 ASN B 173 GLN B 198 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.073972 restraints weight = 42194.987| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.15 r_work: 0.2893 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.239 37425 Z= 0.413 Angle : 2.535 50.586 50799 Z= 1.458 Chirality : 0.452 6.588 5670 Planarity : 0.004 0.060 6330 Dihedral : 9.046 106.867 5474 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 2.07 % Allowed : 18.71 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.99 (0.12), residues: 4558 helix: 1.35 (0.10), residues: 2655 sheet: -0.18 (0.30), residues: 309 loop : -0.24 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 562 TYR 0.022 0.002 TYR L 428 PHE 0.038 0.002 PHE H 277 TRP 0.028 0.001 TRP L 105 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01178 (37389) covalent geometry : angle 2.21844 (50706) hydrogen bonds : bond 0.06131 ( 1662) hydrogen bonds : angle 4.55614 ( 4986) metal coordination : bond 0.04646 ( 36) metal coordination : angle 28.75723 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21442.07 seconds wall clock time: 363 minutes 14.55 seconds (21794.55 seconds total)