Starting phenix.real_space_refine on Mon Jul 6 16:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7t_14537/07_2026/7z7t_14537.map" } resolution = 3.1 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= 0.011 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 11 5.49 5 S 267 5.16 5 C 24335 2.51 5 N 6188 2.21 5 O 6561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37395 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} 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: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4734 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "H" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 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: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 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: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 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: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.108 58.729 193.230 1.00 6.56 S ATOM 2741 SG CYS F 357 74.613 58.512 197.676 1.00 2.75 S ATOM 3062 SG CYS F 398 68.988 54.917 198.213 1.00 1.36 S ATOM 2697 SG CYS F 351 73.534 52.531 194.652 1.00 0.00 S ATOM 4054 SG CYS E 92 81.941 51.034 214.380 1.00 7.50 S ATOM 4088 SG CYS E 97 82.110 51.814 217.888 1.00 5.79 S ATOM 4366 SG CYS E 133 76.874 50.249 214.033 1.00 21.11 S ATOM 4392 SG CYS E 137 75.962 50.946 217.286 1.00 9.07 S ATOM 5476 SG CYS G 114 81.392 65.094 175.823 1.00 2.58 S ATOM 5416 SG CYS G 105 86.442 69.134 177.190 1.00 0.00 S ATOM 5436 SG CYS G 108 87.398 63.149 174.911 1.00 2.97 S ATOM 5830 SG CYS G 156 75.940 57.240 180.692 1.00 4.15 S ATOM 5811 SG CYS G 153 81.761 56.336 183.797 1.00 9.53 S ATOM 5859 SG CYS G 159 79.260 51.656 180.236 1.00 4.70 S ATOM 6207 SG CYS G 203 81.155 56.954 177.149 1.00 23.59 S ATOM 6432 SG CYS G 230 78.256 48.242 155.977 1.00 7.58 S ATOM 6717 SG CYS G 265 78.321 44.521 161.368 1.00 2.84 S ATOM 6480 SG CYS G 237 72.851 47.656 159.127 1.00 16.75 S ATOM 6456 SG CYS G 233 75.342 42.441 156.073 1.00 13.52 S ATOM 4877 SG CYS G 36 69.286 57.855 183.379 1.00 4.11 S ATOM 4953 SG CYS G 47 70.831 61.286 183.753 1.00 1.62 S ATOM 4979 SG CYS G 50 64.961 62.743 183.845 1.00 12.90 S ATOM 5128 SG CYS G 69 64.539 59.236 183.433 1.00 5.75 S ATOM 17234 SG CYS B 129 90.630 92.574 151.620 1.00 21.36 S ATOM 16731 SG CYS B 64 95.723 96.474 153.218 1.00 9.20 S ATOM 16725 SG CYS B 63 90.134 98.304 155.365 1.00 8.17 S ATOM 17451 SG CYS B 158 92.542 92.684 157.518 1.00 12.57 S ATOM 18782 SG CYS I 102 91.467 86.993 163.545 1.00 8.23 S ATOM 18757 SG CYS I 99 96.928 85.729 159.952 1.00 0.00 S ATOM 18800 SG CYS I 105 95.653 82.438 165.340 1.00 10.53 S ATOM 18515 SG CYS I 70 91.750 81.620 160.160 1.00 1.47 S ATOM 18829 SG CYS I 109 96.862 76.879 171.717 1.00 8.23 S ATOM 18492 SG CYS I 66 94.857 76.172 165.572 1.00 2.58 S ATOM 18452 SG CYS I 60 99.129 71.996 167.860 1.00 0.00 S ATOM 18470 SG CYS I 63 92.831 72.282 170.316 1.00 5.90 S Time building chain proxies: 7.45, per 1000 atoms: 0.20 Number of scatterers: 37395 At special positions: 0 Unit cell: (156.88, 218.36, 244.86, 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 267 16.00 P 11 15.00 O 6561 8.00 N 6188 7.00 C 24335 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 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 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " 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="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " 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="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " 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="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8622 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 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 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 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 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 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: 4.882A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.703A 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 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' 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 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: 4.507A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 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 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 5.048A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 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 66 removed outlier: 5.013A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.940A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.292A pdb=" N PHE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 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 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.863A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.658A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.939A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.583A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) 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 132 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: 4.387A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.679A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 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 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.035A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) 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 50 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 157 removed outlier: 4.737A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' 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 395 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 488 Processing helix chain 'M' and resid 491 through 502 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 58 removed outlier: 4.361A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.032A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 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 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' 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: 4.532A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 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 removed outlier: 4.353A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 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 112 removed outlier: 5.174A 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 1716 hydrogen bonds defined for protein. 5148 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: 6.69 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.30: 5872 1.30 - 1.55: 31921 1.55 - 1.80: 367 1.80 - 2.05: 79 2.05 - 2.31: 92 Bond restraints: 38331 Sorted by residual: bond pdb=" CG PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 1.503 1.045 0.458 3.40e-02 8.65e+02 1.82e+02 bond pdb=" N PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.00e+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 8.58e+00 bond pdb=" O13 3PE N 602 " pdb=" P 3PE N 602 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O13 3PE L1301 " pdb=" P 3PE L1301 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.46e+00 ... (remaining 38326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 51856 4.91 - 9.82: 135 9.82 - 14.72: 8 14.72 - 19.63: 2 19.63 - 24.54: 2 Bond angle restraints: 52003 Sorted by residual: angle pdb=" N PRO C 335 " pdb=" CD PRO C 335 " pdb=" CG PRO C 335 " ideal model delta sigma weight residual 103.20 78.66 24.54 1.50e+00 4.44e-01 2.68e+02 angle pdb=" CA PRO C 335 " pdb=" CB PRO C 335 " pdb=" CG PRO C 335 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" CA PRO C 335 " pdb=" N PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 112.00 101.02 10.98 1.40e+00 5.10e-01 6.15e+01 angle pdb=" CA LEU N 242 " pdb=" CB LEU N 242 " pdb=" CG LEU N 242 " ideal model delta sigma weight residual 116.30 136.07 -19.77 3.50e+00 8.16e-02 3.19e+01 angle pdb=" CA LEU B 86 " pdb=" CB LEU B 86 " pdb=" CG LEU B 86 " ideal model delta sigma weight residual 116.30 133.79 -17.49 3.50e+00 8.16e-02 2.50e+01 ... (remaining 51998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 21614 33.94 - 67.88: 759 67.88 - 101.82: 67 101.82 - 135.76: 0 135.76 - 169.70: 1 Dihedral angle restraints: 22441 sinusoidal: 8961 harmonic: 13480 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.89 169.70 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -149.29 -30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA VAL B 85 " pdb=" C VAL B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 22438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 5777 4.246 - 8.492: 0 8.492 - 12.738: 0 12.738 - 16.984: 0 16.984 - 21.230: 28 Chirality restraints: 5805 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.23 2.00e-01 2.50e+01 1.13e+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 10.61 -21.17 2.00e-01 2.50e+01 1.12e+04 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 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5802 not shown) Planarity restraints: 6499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 682 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO G 683 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO G 683 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 683 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 33 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO I 34 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO I 34 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO I 34 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 472 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO L 473 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 473 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 473 " 0.048 5.00e-02 4.00e+02 ... (remaining 6496 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4475 2.75 - 3.29: 36279 3.29 - 3.83: 68898 3.83 - 4.36: 83083 4.36 - 4.90: 139742 Nonbonded interactions: 332477 Sorted by model distance: nonbonded pdb=" O SER G 614 " pdb=" OG SER G 618 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.232 3.040 nonbonded pdb=" O MET B 68 " pdb=" OG SER B 71 " model vdw 2.252 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.255 3.040 ... (remaining 332472 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: 0.570 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: 0.050 Extract box with map and model: 1.050 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 37.930 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.006 0.458 38367 Z= 0.226 Angle : 0.776 24.541 52096 Z= 0.392 Chirality : 1.467 21.230 5805 Planarity : 0.006 0.102 6499 Dihedral : 16.713 169.701 13819 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.23 % Allowed : 19.34 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: -0.38 (0.11), residues: 4679 helix: 0.21 (0.09), residues: 2691 sheet: -0.53 (0.28), residues: 314 loop : -0.76 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 287 TYR 0.029 0.002 TYR N 424 PHE 0.040 0.002 PHE L 341 TRP 0.051 0.001 TRP B 185 HIS 0.009 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (38331) covalent geometry : angle 0.75962 / 0.39 (52003) hydrogen bonds : bond 0.05336 / 3.50 ( 1716) hydrogen bonds : angle 4.71058 / 3.34 ( 5148) metal coordination : bond 0.05482 / 3.51 ( 36) metal coordination : angle 3.87273 / 2.50 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 571 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: H 242 TYR cc_start: 0.8322 (m-80) cc_final: 0.7871 (m-80) REVERT: L 364 LYS cc_start: 0.7308 (tmtt) cc_final: 0.7082 (tptp) REVERT: M 427 PHE cc_start: 0.7587 (m-80) cc_final: 0.7338 (m-80) REVERT: N 482 MET cc_start: 0.5400 (mmt) cc_final: 0.4749 (ttm) REVERT: K 46 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7459 (t80) outliers start: 9 outliers final: 3 residues processed: 576 average time/residue: 0.2591 time to fit residues: 239.6256 Evaluate side-chains 540 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 536 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 238 ASN F 425 GLN G 765 GLN C 56 GLN C 154 ASN C 344 GLN C 359 HIS B 143 GLN I 13 GLN H 152 GLN L 62 GLN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079301 restraints weight = 56456.170| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.05 r_work: 0.2938 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.261 38367 Z= 0.394 Angle : 2.482 50.983 52096 Z= 1.430 Chirality : 0.444 6.533 5805 Planarity : 0.004 0.070 6499 Dihedral : 6.606 176.911 5464 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 18.53 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4679 helix: 0.95 (0.10), residues: 2695 sheet: -0.48 (0.29), residues: 314 loop : -0.54 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 86 TYR 0.023 0.001 TYR L 428 PHE 0.031 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01145 / 0.39 (38331) covalent geometry : angle 2.16609 / 1.43 (52003) hydrogen bonds : bond 0.04567 / 3.01 ( 1716) hydrogen bonds : angle 4.18044 / 2.97 ( 5148) metal coordination : bond 0.05646 / 3.46 ( 36) metal coordination : angle 28.75912 / 20.06 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 578 time to evaluate : 1.616 Fit side-chains REVERT: F 252 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.7985 (t80) REVERT: G 617 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: C 451 ASP cc_start: 0.7666 (t0) cc_final: 0.7166 (t0) REVERT: B 86 LEU cc_start: 0.8211 (tt) cc_final: 0.7966 (tt) REVERT: B 94 ASP cc_start: 0.8108 (m-30) cc_final: 0.7858 (m-30) REVERT: H 242 TYR cc_start: 0.8399 (m-80) cc_final: 0.8019 (m-80) REVERT: M 370 ASP cc_start: 0.8707 (t0) cc_final: 0.8466 (t0) REVERT: N 482 MET cc_start: 0.5076 (mmt) cc_final: 0.4414 (ttm) outliers start: 56 outliers final: 35 residues processed: 615 average time/residue: 0.2453 time to fit residues: 241.6997 Evaluate side-chains 579 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 542 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 408 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 428 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 196 ASN F 237 GLN F 386 GLN F 425 GLN E 78 GLN G 218 ASN C 154 ASN B 52 ASN B 143 GLN I 13 GLN H 45 ASN H 152 GLN H 226 HIS L 232 GLN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN K 5 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.075238 restraints weight = 55809.853| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.03 r_work: 0.2855 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.244 38367 Z= 0.455 Angle : 2.512 50.781 52096 Z= 1.443 Chirality : 0.446 6.532 5805 Planarity : 0.005 0.068 6499 Dihedral : 7.097 177.163 5462 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 3.21 % Allowed : 17.26 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.49 (0.12), residues: 4679 helix: 1.02 (0.10), residues: 2709 sheet: -0.48 (0.29), residues: 311 loop : -0.55 (0.15), residues: 1659 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 0.031 0.002 PHE L 341 TRP 0.015 0.002 TRP L 143 HIS 0.008 0.002 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.01257 / 0.45 (38331) covalent geometry : angle 2.19729 / 1.44 (52003) hydrogen bonds : bond 0.05583 / 3.68 ( 1716) hydrogen bonds : angle 4.34833 / 3.09 ( 5148) metal coordination : bond 0.05258 / 3.10 ( 36) metal coordination : angle 28.87483 / 20.24 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 557 time to evaluate : 1.475 Fit side-chains REVERT: F 252 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8244 (t80) REVERT: E 46 GLN cc_start: 0.8625 (mp10) cc_final: 0.8397 (mp10) REVERT: C 78 HIS cc_start: 0.9330 (OUTLIER) cc_final: 0.9102 (t-90) REVERT: B 65 TYR cc_start: 0.8675 (t80) cc_final: 0.8275 (t80) REVERT: B 91 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7983 (mmt180) REVERT: H 47 TYR cc_start: 0.6337 (m-80) cc_final: 0.5921 (m-80) REVERT: H 242 TYR cc_start: 0.8490 (m-80) cc_final: 0.8279 (m-80) REVERT: L 139 MET cc_start: 0.8349 (ttp) cc_final: 0.8053 (ttp) REVERT: L 482 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.6913 (t) REVERT: M 135 ASP cc_start: 0.7641 (t70) cc_final: 0.7431 (t0) REVERT: N 100 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7629 (t0) REVERT: N 482 MET cc_start: 0.5744 (mmt) cc_final: 0.4782 (ttm) outliers start: 124 outliers final: 73 residues processed: 645 average time/residue: 0.2541 time to fit residues: 264.6224 Evaluate side-chains 621 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 543 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 901 HIS Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 159 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 303 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 262 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 287 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN C 135 ASN C 154 ASN C 344 GLN I 13 GLN H 45 ASN H 152 GLN H 226 HIS ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.077774 restraints weight = 55694.796| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.04 r_work: 0.2907 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38367 Z= 0.389 Angle : 2.487 50.846 52096 Z= 1.432 Chirality : 0.442 6.442 5805 Planarity : 0.004 0.062 6499 Dihedral : 6.703 178.610 5460 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 2.36 % Allowed : 18.38 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.82 (0.12), residues: 4679 helix: 1.33 (0.10), residues: 2704 sheet: -0.48 (0.30), residues: 302 loop : -0.47 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 86 TYR 0.024 0.001 TYR M 435 PHE 0.030 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01134 / 0.39 (38331) covalent geometry : angle 2.16821 / 1.43 (52003) hydrogen bonds : bond 0.04630 / 3.05 ( 1716) hydrogen bonds : angle 4.11400 / 2.92 ( 5148) metal coordination : bond 0.03173 / 1.93 ( 36) metal coordination : angle 28.92924 / 20.38 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 569 time to evaluate : 1.406 Fit side-chains REVERT: F 252 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8120 (t80) REVERT: G 11 LYS cc_start: 0.8649 (tptp) cc_final: 0.8139 (tttm) REVERT: G 56 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7998 (mm-40) REVERT: G 855 ASN cc_start: 0.8358 (m-40) cc_final: 0.8088 (m-40) REVERT: C 39 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 163 THR cc_start: 0.8366 (p) cc_final: 0.8149 (p) REVERT: C 597 ASP cc_start: 0.8200 (t0) cc_final: 0.7998 (t0) REVERT: B 65 TYR cc_start: 0.8518 (t80) cc_final: 0.8278 (t80) REVERT: B 91 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7989 (mmt180) REVERT: H 242 TYR cc_start: 0.8394 (m-80) cc_final: 0.8126 (m-80) REVERT: A 124 ASP cc_start: 0.8368 (t0) cc_final: 0.7849 (t0) REVERT: L 482 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.6867 (t) REVERT: L 569 MET cc_start: 0.8393 (mmm) cc_final: 0.8019 (mmp) REVERT: M 150 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7820 (mtp) REVERT: N 100 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7484 (t0) REVERT: N 482 MET cc_start: 0.5669 (mmt) cc_final: 0.4609 (ttm) outliers start: 91 outliers final: 52 residues processed: 630 average time/residue: 0.2489 time to fit residues: 253.8781 Evaluate side-chains 593 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 535 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 97 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN G 218 ASN ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN H 45 ASN H 152 GLN H 226 HIS L 62 GLN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.075364 restraints weight = 55343.231| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.02 r_work: 0.2858 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38367 Z= 0.444 Angle : 2.508 50.735 52096 Z= 1.441 Chirality : 0.445 6.501 5805 Planarity : 0.005 0.063 6499 Dihedral : 7.094 177.148 5460 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.08 % Allowed : 17.83 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.66 (0.12), residues: 4679 helix: 1.18 (0.10), residues: 2716 sheet: -0.55 (0.30), residues: 312 loop : -0.51 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 37 TYR 0.021 0.002 TYR L 428 PHE 0.029 0.002 PHE L 341 TRP 0.016 0.002 TRP L 143 HIS 0.008 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.01239 / 0.44 (38331) covalent geometry : angle 2.19318 / 1.44 (52003) hydrogen bonds : bond 0.05411 / 3.56 ( 1716) hydrogen bonds : angle 4.30080 / 3.05 ( 5148) metal coordination : bond 0.04429 / 2.72 ( 36) metal coordination : angle 28.89619 / 20.35 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 553 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: F 252 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8280 (t80) REVERT: E 46 GLN cc_start: 0.8571 (mp10) cc_final: 0.8346 (mp10) REVERT: G 56 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8061 (mm-40) REVERT: C 163 THR cc_start: 0.8364 (p) cc_final: 0.8161 (p) REVERT: C 307 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8341 (mtt180) REVERT: C 585 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.7850 (mm) REVERT: B 65 TYR cc_start: 0.8625 (t80) cc_final: 0.8238 (t80) REVERT: B 91 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7920 (mmt180) REVERT: B 94 ASP cc_start: 0.8295 (m-30) cc_final: 0.7971 (m-30) REVERT: H 47 TYR cc_start: 0.6304 (m-80) cc_final: 0.5778 (m-80) REVERT: H 238 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5799 (m-10) REVERT: H 279 MET cc_start: 0.7804 (mtt) cc_final: 0.7554 (mtt) REVERT: L 139 MET cc_start: 0.8350 (ttp) cc_final: 0.8083 (ttp) REVERT: L 482 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7036 (t) REVERT: M 150 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: N 100 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7545 (t0) outliers start: 119 outliers final: 87 residues processed: 641 average time/residue: 0.2547 time to fit residues: 263.4216 Evaluate side-chains 628 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 533 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 126 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN E 78 GLN G 218 ASN ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 883 GLN C 344 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN H 152 GLN H 226 HIS H 261 GLN L 62 GLN L 409 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077036 restraints weight = 55328.479| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.02 r_work: 0.2894 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38367 Z= 0.394 Angle : 2.494 50.953 52096 Z= 1.434 Chirality : 0.441 6.471 5805 Planarity : 0.004 0.063 6499 Dihedral : 6.867 177.960 5460 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 2.95 % Allowed : 18.27 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.86 (0.12), residues: 4679 helix: 1.39 (0.10), residues: 2699 sheet: -0.55 (0.30), residues: 292 loop : -0.48 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 160 TYR 0.022 0.001 TYR M 435 PHE 0.030 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01145 / 0.39 (38331) covalent geometry : angle 2.17410 / 1.43 (52003) hydrogen bonds : bond 0.04807 / 3.17 ( 1716) hydrogen bonds : angle 4.16924 / 2.96 ( 5148) metal coordination : bond 0.03312 / 2.08 ( 36) metal coordination : angle 28.99371 / 20.49 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 553 time to evaluate : 1.470 Fit side-chains REVERT: F 252 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8252 (t80) REVERT: G 56 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8036 (mm-40) REVERT: G 429 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8050 (m-70) REVERT: C 39 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 78 HIS cc_start: 0.9288 (OUTLIER) cc_final: 0.9046 (t-90) REVERT: C 163 THR cc_start: 0.8377 (p) cc_final: 0.8170 (p) REVERT: C 307 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8310 (mtt180) REVERT: B 65 TYR cc_start: 0.8543 (t80) cc_final: 0.8274 (t80) REVERT: B 91 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7928 (mmt180) REVERT: B 94 ASP cc_start: 0.8261 (m-30) cc_final: 0.7926 (m-30) REVERT: B 112 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7822 (tmm-80) REVERT: H 238 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5821 (m-10) REVERT: H 279 MET cc_start: 0.7780 (mtt) cc_final: 0.7546 (mtt) REVERT: A 124 ASP cc_start: 0.8435 (t0) cc_final: 0.7942 (t0) REVERT: L 77 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: L 482 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.6917 (t) REVERT: L 569 MET cc_start: 0.8369 (mmm) cc_final: 0.8002 (mmp) REVERT: L 577 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7770 (mtp180) REVERT: M 38 LEU cc_start: 0.8483 (tp) cc_final: 0.8134 (mt) REVERT: M 150 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7834 (mtp) REVERT: N 100 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7454 (t0) REVERT: N 482 MET cc_start: 0.5612 (mmt) cc_final: 0.4735 (ttm) outliers start: 114 outliers final: 84 residues processed: 636 average time/residue: 0.2403 time to fit residues: 247.4450 Evaluate side-chains 631 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 535 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 427 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 334 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 456 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN G 218 ASN ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN H 45 ASN H 152 GLN H 226 HIS H 261 GLN L 62 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.075802 restraints weight = 55488.881| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.02 r_work: 0.2866 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38367 Z= 0.426 Angle : 2.504 50.767 52096 Z= 1.439 Chirality : 0.444 6.501 5805 Planarity : 0.005 0.065 6499 Dihedral : 7.083 177.090 5460 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 3.50 % Allowed : 18.17 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.75 (0.12), residues: 4679 helix: 1.28 (0.10), residues: 2711 sheet: -0.58 (0.30), residues: 302 loop : -0.50 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 86 TYR 0.021 0.002 TYR L 428 PHE 0.029 0.002 PHE L 341 TRP 0.016 0.001 TRP A 88 HIS 0.007 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.01203 / 0.42 (38331) covalent geometry : angle 2.18712 / 1.44 (52003) hydrogen bonds : bond 0.05202 / 3.43 ( 1716) hydrogen bonds : angle 4.27187 / 3.04 ( 5148) metal coordination : bond 0.04045 / 2.53 ( 36) metal coordination : angle 28.96275 / 20.46 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 545 time to evaluate : 1.005 Fit side-chains REVERT: F 252 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8282 (t80) REVERT: G 56 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8063 (mm-40) REVERT: C 39 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8728 (p) REVERT: C 78 HIS cc_start: 0.9323 (OUTLIER) cc_final: 0.9089 (t-90) REVERT: C 163 THR cc_start: 0.8382 (p) cc_final: 0.8181 (p) REVERT: C 307 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8356 (mtt180) REVERT: B 65 TYR cc_start: 0.8585 (t80) cc_final: 0.8198 (t80) REVERT: B 91 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7941 (mmt180) REVERT: B 112 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7785 (tmm-80) REVERT: H 238 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5800 (m-10) REVERT: L 77 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: L 139 MET cc_start: 0.8365 (ttp) cc_final: 0.8071 (ttp) REVERT: L 482 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7062 (t) REVERT: L 569 MET cc_start: 0.8402 (mmm) cc_final: 0.8018 (mmp) REVERT: M 38 LEU cc_start: 0.8496 (tp) cc_final: 0.8152 (mt) REVERT: M 150 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7865 (mtp) REVERT: M 373 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7610 (mpp) REVERT: N 100 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7478 (t0) outliers start: 135 outliers final: 102 residues processed: 642 average time/residue: 0.2338 time to fit residues: 243.9856 Evaluate side-chains 647 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 533 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 314 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 442 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN G 218 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN H 152 GLN H 226 HIS H 261 GLN H 312 ASN L 62 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.076453 restraints weight = 55001.823| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.01 r_work: 0.2881 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38367 Z= 0.407 Angle : 2.499 50.780 52096 Z= 1.436 Chirality : 0.443 6.484 5805 Planarity : 0.004 0.064 6499 Dihedral : 7.059 177.322 5460 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 3.14 % Allowed : 18.40 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.80 (0.12), residues: 4679 helix: 1.33 (0.10), residues: 2707 sheet: -0.58 (0.31), residues: 291 loop : -0.49 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 86 TYR 0.022 0.002 TYR L 428 PHE 0.030 0.002 PHE L 341 TRP 0.020 0.001 TRP A 88 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01167 / 0.41 (38331) covalent geometry : angle 2.17964 / 1.43 (52003) hydrogen bonds : bond 0.04983 / 3.28 ( 1716) hydrogen bonds : angle 4.22938 / 3.01 ( 5148) metal coordination : bond 0.03619 / 2.28 ( 36) metal coordination : angle 28.99599 / 20.51 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 545 time to evaluate : 0.970 Fit side-chains REVERT: F 252 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8270 (t80) REVERT: G 56 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8092 (mm-40) REVERT: G 429 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8166 (m-70) REVERT: C 78 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.9059 (t-90) REVERT: C 163 THR cc_start: 0.8371 (p) cc_final: 0.8171 (p) REVERT: C 307 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8321 (mtt180) REVERT: B 65 TYR cc_start: 0.8561 (t80) cc_final: 0.8239 (t80) REVERT: B 91 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7948 (mmt180) REVERT: B 112 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7788 (tmm-80) REVERT: H 238 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5711 (m-10) REVERT: A 124 ASP cc_start: 0.8445 (t0) cc_final: 0.7965 (t0) REVERT: L 77 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: L 139 MET cc_start: 0.8322 (ttp) cc_final: 0.8053 (ttp) REVERT: L 482 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7073 (t) REVERT: L 569 MET cc_start: 0.8397 (mmm) cc_final: 0.8035 (mmp) REVERT: M 38 LEU cc_start: 0.8504 (tp) cc_final: 0.8151 (mt) REVERT: M 150 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: N 100 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7437 (t0) REVERT: N 217 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8880 (mmtp) outliers start: 121 outliers final: 101 residues processed: 637 average time/residue: 0.2379 time to fit residues: 246.4225 Evaluate side-chains 648 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 536 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 419 optimal weight: 0.9990 chunk 429 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 437 optimal weight: 6.9990 chunk 402 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN G 218 ASN B 143 GLN H 45 ASN H 152 GLN H 226 HIS H 261 GLN H 312 ASN L 62 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077491 restraints weight = 55607.526| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.02 r_work: 0.2901 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38367 Z= 0.392 Angle : 2.494 50.776 52096 Z= 1.434 Chirality : 0.442 6.464 5805 Planarity : 0.004 0.063 6499 Dihedral : 6.881 177.331 5460 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 2.85 % Allowed : 18.66 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.93 (0.12), residues: 4679 helix: 1.45 (0.10), residues: 2699 sheet: -0.51 (0.31), residues: 284 loop : -0.45 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 86 TYR 0.024 0.001 TYR M 435 PHE 0.031 0.001 PHE L 341 TRP 0.026 0.001 TRP A 88 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.39 (38331) covalent geometry : angle 2.17310 / 1.43 (52003) hydrogen bonds : bond 0.04662 / 3.07 ( 1716) hydrogen bonds : angle 4.14585 / 2.95 ( 5148) metal coordination : bond 0.03103 / 1.99 ( 36) metal coordination : angle 29.03901 / 20.56 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 551 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: F 252 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8216 (t80) REVERT: G 56 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8073 (mm-40) REVERT: G 429 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: B 65 TYR cc_start: 0.8502 (t80) cc_final: 0.8235 (t80) REVERT: B 91 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7939 (mmt180) REVERT: I 32 MET cc_start: 0.7784 (mmm) cc_final: 0.7464 (mmm) REVERT: H 238 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: A 124 ASP cc_start: 0.8410 (t0) cc_final: 0.7947 (t0) REVERT: L 77 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: L 569 MET cc_start: 0.8381 (mmm) cc_final: 0.8066 (mmp) REVERT: M 38 LEU cc_start: 0.8502 (tp) cc_final: 0.8143 (mt) REVERT: M 150 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: N 100 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7389 (t0) REVERT: N 217 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8879 (mmtp) outliers start: 110 outliers final: 95 residues processed: 633 average time/residue: 0.2388 time to fit residues: 245.1173 Evaluate side-chains 637 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 535 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 104 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 368 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 399 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN G 218 ASN ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 152 GLN H 226 HIS H 261 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.077116 restraints weight = 55250.641| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.02 r_work: 0.2893 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38367 Z= 0.399 Angle : 2.497 50.761 52096 Z= 1.435 Chirality : 0.442 6.470 5805 Planarity : 0.004 0.063 6499 Dihedral : 6.918 176.851 5460 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 2.85 % Allowed : 18.69 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.94 (0.12), residues: 4679 helix: 1.46 (0.10), residues: 2693 sheet: -0.48 (0.32), residues: 284 loop : -0.45 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 86 TYR 0.022 0.002 TYR M 435 PHE 0.030 0.001 PHE L 341 TRP 0.022 0.001 TRP A 88 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.40 (38331) covalent geometry : angle 2.17696 / 1.43 (52003) hydrogen bonds : bond 0.04776 / 3.14 ( 1716) hydrogen bonds : angle 4.15723 / 2.96 ( 5148) metal coordination : bond 0.03352 / 2.12 ( 36) metal coordination : angle 29.00875 / 20.54 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 535 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: F 252 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8193 (t80) REVERT: G 56 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8111 (mm-40) REVERT: G 429 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8088 (m-70) REVERT: B 65 TYR cc_start: 0.8530 (t80) cc_final: 0.8154 (t80) REVERT: B 91 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7940 (mmt180) REVERT: B 112 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7873 (tmm-80) REVERT: I 32 MET cc_start: 0.7831 (mmm) cc_final: 0.7530 (mmm) REVERT: H 238 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5745 (m-10) REVERT: A 124 ASP cc_start: 0.8296 (t0) cc_final: 0.7747 (t70) REVERT: L 77 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: L 482 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.6972 (t) REVERT: L 569 MET cc_start: 0.8391 (mmm) cc_final: 0.8049 (mmp) REVERT: M 38 LEU cc_start: 0.8504 (tp) cc_final: 0.8144 (mt) REVERT: M 150 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: M 373 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7730 (mpp) REVERT: N 100 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7398 (t0) REVERT: N 217 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8887 (mmtp) REVERT: N 347 MET cc_start: 0.8124 (mpp) cc_final: 0.7774 (mpp) outliers start: 110 outliers final: 96 residues processed: 618 average time/residue: 0.2324 time to fit residues: 233.2462 Evaluate side-chains 639 residues out of total 3860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 533 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 429 HIS Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 646 VAL Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 762 ASN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 902 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 574 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 489 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 130 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 440 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 425 GLN G 224 GLN ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN H 45 ASN H 152 GLN H 226 HIS H 261 GLN H 312 ASN L 62 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.078684 restraints weight = 55618.754| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.03 r_work: 0.2924 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38367 Z= 0.385 Angle : 2.492 50.772 52096 Z= 1.432 Chirality : 0.441 6.448 5805 Planarity : 0.004 0.062 6499 Dihedral : 6.719 177.355 5460 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 2.33 % Allowed : 19.31 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4679 helix: 1.57 (0.10), residues: 2691 sheet: -0.38 (0.32), residues: 284 loop : -0.39 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 86 TYR 0.025 0.001 TYR M 435 PHE 0.031 0.001 PHE L 341 TRP 0.034 0.001 TRP A 88 HIS 0.008 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.38 (38331) covalent geometry : angle 2.16953 / 1.43 (52003) hydrogen bonds : bond 0.04407 / 2.90 ( 1716) hydrogen bonds : angle 4.06065 / 2.89 ( 5148) metal coordination : bond 0.02634 / 1.71 ( 36) metal coordination : angle 29.09672 / 20.63 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12460.94 seconds wall clock time: 213 minutes 10.94 seconds (12790.94 seconds total)