Starting phenix.real_space_refine on Sat Mar 7 00:43:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p62_13215/03_2026/7p62_13215.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p62_13215/03_2026/7p62_13215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p62_13215/03_2026/7p62_13215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p62_13215/03_2026/7p62_13215.map" model { file = "/net/cci-nas-00/data/ceres_data/7p62_13215/03_2026/7p62_13215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p62_13215/03_2026/7p62_13215.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.034 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 3 5.49 5 S 266 5.16 5 C 23760 2.51 5 N 6090 2.21 5 O 6445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36597 Number of models: 1 Model: "" Number of chains: 19 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4644 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 538} Chain breaks: 2 Chain: "B" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1529 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 178} Chain breaks: 3 Chain: "I" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1140 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "L" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4530 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 576} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 482} Chain: "N" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2422 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1312 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 70.227 61.343 195.693 1.00 72.41 S ATOM 2766 SG CYS F 357 73.713 61.382 200.392 1.00 62.06 S ATOM 3087 SG CYS F 398 68.003 57.984 200.878 1.00 61.07 S ATOM 2722 SG CYS F 351 72.530 55.298 197.490 1.00 38.66 S ATOM 4079 SG CYS E 92 81.233 53.588 217.380 1.00 95.27 S ATOM 4113 SG CYS E 97 81.128 54.463 220.799 1.00 86.52 S ATOM 4391 SG CYS E 133 76.459 52.654 216.479 1.00 79.11 S ATOM 4417 SG CYS E 137 75.156 53.566 219.927 1.00 88.78 S ATOM 5501 SG CYS G 114 80.931 66.816 178.092 1.00 44.59 S ATOM 5441 SG CYS G 105 86.259 70.401 179.944 1.00 73.92 S ATOM 5461 SG CYS G 108 86.824 64.512 177.379 1.00 31.55 S ATOM 5855 SG CYS G 156 74.889 59.329 183.411 1.00 68.70 S ATOM 5836 SG CYS G 153 80.736 58.504 186.377 1.00 39.33 S ATOM 5884 SG CYS G 159 77.999 53.620 183.010 1.00 35.66 S ATOM 6228 SG CYS G 203 80.100 58.669 179.772 1.00 63.71 S ATOM 6453 SG CYS G 230 76.891 49.222 158.850 1.00 60.79 S ATOM 6738 SG CYS G 265 76.791 45.831 164.474 1.00 55.13 S ATOM 6501 SG CYS G 237 71.523 48.998 162.048 1.00 58.15 S ATOM 6477 SG CYS G 233 73.882 43.462 159.243 1.00 94.24 S ATOM 4902 SG CYS G 36 68.608 60.415 186.012 1.00 38.38 S ATOM 4978 SG CYS G 47 70.019 63.642 186.524 1.00 35.57 S ATOM 5004 SG CYS G 50 64.188 65.304 186.143 1.00 92.28 S ATOM 5153 SG CYS G 69 63.924 61.453 185.902 1.00 65.53 S ATOM 17125 SG CYS B 129 92.011 93.349 153.530 1.00 72.15 S ATOM 16737 SG CYS B 64 96.931 97.814 154.754 1.00113.88 S ATOM 16731 SG CYS B 63 90.796 99.099 156.084 1.00119.36 S ATOM 17342 SG CYS B 158 93.552 94.320 159.440 1.00 92.82 S ATOM 18377 SG CYS I 102 91.615 87.711 165.481 1.00 50.55 S ATOM 18352 SG CYS I 99 96.930 86.174 161.741 1.00 60.38 S ATOM 18395 SG CYS I 105 95.766 83.096 167.308 1.00 35.38 S ATOM 18110 SG CYS I 70 91.754 82.304 162.115 1.00 58.64 S ATOM 18424 SG CYS I 109 96.748 77.717 173.976 1.00 36.79 S ATOM 18087 SG CYS I 66 94.794 76.864 167.847 1.00 48.87 S ATOM 18047 SG CYS I 60 99.132 72.687 170.419 1.00 28.65 S ATOM 18065 SG CYS I 63 92.787 72.970 172.480 1.00 21.83 S Time building chain proxies: 7.91, per 1000 atoms: 0.22 Number of scatterers: 36597 At special positions: 0 Unit cell: (158.089, 215.383, 250.396, 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 266 16.00 P 3 15.00 O 6445 8.00 N 6090 7.00 C 23760 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: 3.13 Conformation dependent library (CDL) restraints added in 1.8 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="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " 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="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8544 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 52.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.928A pdb=" N ASP F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 302 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.395A pdb=" N SER E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.065A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.838A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 276 removed outlier: 5.447A pdb=" N TYR G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR G 274 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.504A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.174A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 605 removed outlier: 6.430A pdb=" N ASN G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 605' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 5.307A pdb=" N GLY G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE G 688 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS G 689 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP G 690 " --> pdb=" O ALA G 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 683 through 690' Processing helix chain 'G' and resid 764 through 768 removed outlier: 5.701A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 768' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.326A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 5.774A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 420 removed outlier: 5.146A pdb=" N LEU C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 removed outlier: 3.999A pdb=" N VAL C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 63 through 68 removed outlier: 5.551A pdb=" N GLU B 67 " --> pdb=" O CYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'H' and resid 6 through 39 removed outlier: 3.797A pdb=" N PHE H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 69 removed outlier: 4.607A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 100 removed outlier: 5.029A pdb=" N THR H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) Proline residue: H 87 - end of helix removed outlier: 4.717A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 5.211A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.128A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 231 through 257 removed outlier: 3.946A pdb=" N PHE H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR H 242 " --> pdb=" O PHE H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 removed outlier: 4.631A pdb=" N CYS H 305 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 removed outlier: 5.397A pdb=" N ALA A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.557A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'L' and resid 4 through 20 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 removed outlier: 4.345A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 removed outlier: 3.630A pdb=" N GLU L 202 " --> pdb=" O ARG L 198 " (cutoff:3.500A) Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 removed outlier: 6.533A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA L 218 " --> pdb=" O MET L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.612A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 removed outlier: 4.120A pdb=" N ALA L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 removed outlier: 4.312A pdb=" N VAL L 436 " --> pdb=" O MET L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 511 removed outlier: 4.116A pdb=" N THR L 492 " --> pdb=" O GLY L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 560 removed outlier: 5.474A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 49 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 233 removed outlier: 6.324A pdb=" N TYR M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 256 through 262 Processing helix chain 'M' and resid 266 through 275 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 501 removed outlier: 4.823A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.233A pdb=" N ILE N 9 " --> pdb=" O PRO N 5 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA N 10 " --> pdb=" O GLN N 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 5 through 10' Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.146A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix removed outlier: 4.049A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.960A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.446A pdb=" N VAL N 271 " --> pdb=" O GLU N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 320 through 347 removed outlier: 6.137A pdb=" N GLU N 324 " --> pdb=" O GLU N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.117A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.966A 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 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 111 removed outlier: 4.970A 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 1654 hydrogen bonds defined for protein. 4962 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: 6.50 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15684 1.42 - 1.64: 21336 1.64 - 1.87: 407 1.87 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37519 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.384 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C THR F 355 " pdb=" N PRO F 356 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.372 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C ILE H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.23e-02 6.61e+03 1.18e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 37514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 50148 2.68 - 5.35: 644 5.35 - 8.03: 145 8.03 - 10.70: 39 10.70 - 13.38: 13 Bond angle restraints: 50989 Sorted by residual: angle pdb=" CA PRO G 840 " pdb=" N PRO G 840 " pdb=" CD PRO G 840 " ideal model delta sigma weight residual 112.00 104.17 7.83 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CA PRO M 61 " pdb=" N PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 112.00 104.29 7.71 1.40e+00 5.10e-01 3.03e+01 angle pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta sigma weight residual 122.61 130.42 -7.81 1.56e+00 4.11e-01 2.51e+01 angle pdb=" C LEU M 264 " pdb=" CA LEU M 264 " pdb=" CB LEU M 264 " ideal model delta sigma weight residual 117.23 110.43 6.80 1.36e+00 5.41e-01 2.50e+01 angle pdb=" N MET C 387 " pdb=" CA MET C 387 " pdb=" C MET C 387 " ideal model delta sigma weight residual 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 ... (remaining 50984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.49: 19769 19.49 - 38.98: 1817 38.98 - 58.47: 325 58.47 - 77.96: 46 77.96 - 97.45: 11 Dihedral angle restraints: 21968 sinusoidal: 8615 harmonic: 13353 Sorted by residual: dihedral pdb=" CA CYS B 158 " pdb=" C CYS B 158 " pdb=" N PRO B 159 " pdb=" CA PRO B 159 " ideal model delta harmonic sigma weight residual -180.00 -120.35 -59.65 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA PRO F 201 " pdb=" C PRO F 201 " pdb=" N PRO F 202 " pdb=" CA PRO F 202 " ideal model delta harmonic sigma weight residual 180.00 149.38 30.62 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA MET H 32 " pdb=" C MET H 32 " pdb=" N SER H 33 " pdb=" CA SER H 33 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 21965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5711 4.238 - 8.476: 0 8.476 - 12.714: 0 12.714 - 16.951: 0 16.951 - 21.189: 28 Chirality restraints: 5739 Sorted by residual: chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.19 2.00e-01 2.50e+01 1.12e+04 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 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5736 not shown) Planarity restraints: 6411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 60 " -0.108 5.00e-02 4.00e+02 1.62e-01 4.18e+01 pdb=" N PRO M 61 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO M 61 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO M 61 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 839 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO G 840 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO G 840 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 840 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 4 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO N 5 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.053 5.00e-02 4.00e+02 ... (remaining 6408 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3996 2.75 - 3.29: 36111 3.29 - 3.83: 65861 3.83 - 4.36: 76606 4.36 - 4.90: 131941 Nonbonded interactions: 314515 Sorted by model distance: nonbonded pdb=" OG SER G 739 " pdb=" OE1 GLU G 741 " model vdw 2.217 3.040 nonbonded pdb=" O TYR N 159 " pdb=" OG SER N 163 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.250 3.040 nonbonded pdb=" O ALA M 316 " pdb=" OG SER M 319 " model vdw 2.254 3.040 ... (remaining 314510 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 37555 Z= 0.195 Angle : 0.843 13.381 51082 Z= 0.422 Chirality : 1.477 21.189 5739 Planarity : 0.007 0.162 6411 Dihedral : 15.051 97.451 13424 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.45 % Allowed : 16.58 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -1.26 (0.11), residues: 4629 helix: -0.19 (0.10), residues: 2561 sheet: -0.99 (0.29), residues: 288 loop : -1.66 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 160 TYR 0.040 0.002 TYR M 435 PHE 0.034 0.002 PHE H 277 TRP 0.037 0.001 TRP C 386 HIS 0.008 0.001 HIS G 429 Details of bonding type rmsd covalent geometry : bond 0.00399 (37519) covalent geometry : angle 0.83045 (50989) hydrogen bonds : bond 0.04548 ( 1654) hydrogen bonds : angle 4.76906 ( 4962) metal coordination : bond 0.05587 ( 36) metal coordination : angle 3.43450 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 527 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 MET cc_start: 0.8302 (mtp) cc_final: 0.8002 (mtt) REVERT: E 144 MET cc_start: 0.9198 (mtm) cc_final: 0.8873 (mtp) REVERT: G 310 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8512 (mm-40) REVERT: G 728 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7720 (pt0) REVERT: G 855 ASN cc_start: 0.8465 (t0) cc_final: 0.7971 (p0) REVERT: C 62 ASP cc_start: 0.8772 (t0) cc_final: 0.8363 (t0) REVERT: C 273 ASP cc_start: 0.8436 (m-30) cc_final: 0.8138 (m-30) REVERT: B 27 ASP cc_start: 0.8159 (p0) cc_final: 0.7620 (p0) REVERT: B 135 MET cc_start: 0.8518 (ptm) cc_final: 0.8306 (ttp) REVERT: B 178 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8646 (mtpp) REVERT: I 119 ASP cc_start: 0.8445 (t0) cc_final: 0.8238 (t0) REVERT: I 124 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8637 (mm-30) REVERT: L 43 LEU cc_start: 0.8537 (mm) cc_final: 0.8301 (tt) REVERT: L 319 MET cc_start: 0.8249 (mmt) cc_final: 0.7987 (mmt) REVERT: L 476 GLN cc_start: 0.8543 (mp10) cc_final: 0.7959 (pm20) REVERT: M 223 LEU cc_start: 0.9118 (mt) cc_final: 0.8887 (mt) REVERT: M 439 MET cc_start: 0.9054 (tmm) cc_final: 0.8805 (tmm) REVERT: N 61 MET cc_start: 0.8172 (ptm) cc_final: 0.7839 (pmm) REVERT: N 306 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (mm) REVERT: H 165 MET cc_start: 0.7932 (mmt) cc_final: 0.7695 (mmp) REVERT: H 229 TYR cc_start: 0.9271 (m-80) cc_final: 0.8778 (m-10) REVERT: H 241 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6933 (tm-30) REVERT: A 85 LEU cc_start: 0.8530 (mt) cc_final: 0.7417 (mp) REVERT: A 94 GLU cc_start: 0.9400 (mp0) cc_final: 0.9120 (mp0) REVERT: J 44 PHE cc_start: 0.8987 (m-80) cc_final: 0.8629 (m-10) REVERT: J 73 MET cc_start: 0.8847 (ttm) cc_final: 0.8557 (ttm) REVERT: J 86 GLN cc_start: 0.8678 (mm110) cc_final: 0.8461 (mm110) REVERT: J 87 TRP cc_start: 0.8502 (p90) cc_final: 0.8242 (p90) REVERT: J 89 LYS cc_start: 0.7636 (mmtm) cc_final: 0.7149 (mmtt) outliers start: 17 outliers final: 8 residues processed: 538 average time/residue: 0.2321 time to fit residues: 206.6507 Evaluate side-chains 492 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 483 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain J residue 74 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 432 optimal weight: 0.0670 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0010 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 overall best weight: 2.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS G 416 GLN C 56 GLN B 52 ASN L 163 ASN M 339 GLN M 348 HIS H 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.061173 restraints weight = 77551.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.062835 restraints weight = 46069.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.063939 restraints weight = 32839.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.064683 restraints weight = 26158.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065165 restraints weight = 22338.051| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37555 Z= 0.400 Angle : 2.527 50.747 51082 Z= 1.451 Chirality : 0.444 6.572 5739 Planarity : 0.005 0.112 6411 Dihedral : 5.890 95.785 5168 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.89 % Allowed : 15.87 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.48 (0.12), residues: 4629 helix: 0.54 (0.10), residues: 2588 sheet: -0.89 (0.29), residues: 304 loop : -1.46 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 160 TYR 0.024 0.001 TYR L 428 PHE 0.025 0.001 PHE L 430 TRP 0.033 0.001 TRP C 386 HIS 0.006 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.01162 (37519) covalent geometry : angle 2.20569 (50989) hydrogen bonds : bond 0.04100 ( 1654) hydrogen bonds : angle 4.18150 ( 4962) metal coordination : bond 0.05013 ( 36) metal coordination : angle 28.97835 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 495 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: F 159 ASN cc_start: 0.7987 (t0) cc_final: 0.7632 (t0) REVERT: E 78 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: G 301 MET cc_start: 0.8183 (mmp) cc_final: 0.7947 (mmp) REVERT: G 308 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8865 (mp) REVERT: C 62 ASP cc_start: 0.7607 (t0) cc_final: 0.6864 (t0) REVERT: C 110 ASP cc_start: 0.7186 (p0) cc_final: 0.6955 (p0) REVERT: C 424 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8932 (m) REVERT: B 178 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8477 (mmtt) REVERT: L 43 LEU cc_start: 0.8761 (mm) cc_final: 0.8552 (tt) REVERT: L 216 MET cc_start: 0.8058 (mtt) cc_final: 0.7548 (mtt) REVERT: L 424 MET cc_start: 0.7487 (ppp) cc_final: 0.7121 (ppp) REVERT: L 430 PHE cc_start: 0.7034 (t80) cc_final: 0.6829 (t80) REVERT: M 153 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8679 (mp) REVERT: M 323 MET cc_start: 0.8190 (mmm) cc_final: 0.7804 (mmm) REVERT: N 200 GLU cc_start: 0.7481 (tt0) cc_final: 0.7257 (mt-10) REVERT: N 217 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8323 (mmtt) REVERT: H 73 TRP cc_start: 0.7111 (t60) cc_final: 0.6791 (t60) REVERT: H 165 MET cc_start: 0.7697 (mmt) cc_final: 0.7469 (mmp) REVERT: H 229 TYR cc_start: 0.9088 (m-80) cc_final: 0.8581 (m-10) REVERT: A 85 LEU cc_start: 0.8637 (mt) cc_final: 0.8093 (mt) outliers start: 72 outliers final: 39 residues processed: 550 average time/residue: 0.2222 time to fit residues: 202.0944 Evaluate side-chains 511 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 468 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 203 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 403 optimal weight: 0.9990 chunk 462 optimal weight: 20.0000 chunk 250 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 388 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 375 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS I 168 ASN L 301 GLN L 438 HIS M 322 HIS N 7 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.060228 restraints weight = 76810.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.061837 restraints weight = 45658.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.062932 restraints weight = 32742.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063667 restraints weight = 26198.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.064167 restraints weight = 22452.533| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.250 37555 Z= 0.394 Angle : 2.525 50.782 51082 Z= 1.450 Chirality : 0.443 6.424 5739 Planarity : 0.004 0.094 6411 Dihedral : 5.601 90.687 5158 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.67 % Allowed : 15.68 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.10 (0.12), residues: 4629 helix: 0.90 (0.10), residues: 2590 sheet: -0.93 (0.30), residues: 305 loop : -1.35 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 160 TYR 0.023 0.001 TYR M 435 PHE 0.023 0.001 PHE L 430 TRP 0.031 0.001 TRP C 386 HIS 0.004 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01150 (37519) covalent geometry : angle 2.20058 (50989) hydrogen bonds : bond 0.04020 ( 1654) hydrogen bonds : angle 4.06553 ( 4962) metal coordination : bond 0.02975 ( 36) metal coordination : angle 29.10348 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 492 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: F 159 ASN cc_start: 0.7987 (t0) cc_final: 0.7679 (t0) REVERT: F 386 GLN cc_start: 0.8579 (tt0) cc_final: 0.8310 (tt0) REVERT: E 78 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: G 171 ASP cc_start: 0.8219 (t0) cc_final: 0.7717 (t0) REVERT: G 301 MET cc_start: 0.8250 (mmp) cc_final: 0.8031 (mmp) REVERT: G 308 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 110 ASP cc_start: 0.7275 (p0) cc_final: 0.7073 (p0) REVERT: C 424 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8876 (m) REVERT: L 216 MET cc_start: 0.8017 (mtt) cc_final: 0.7610 (mtt) REVERT: L 424 MET cc_start: 0.7424 (ppp) cc_final: 0.6908 (ppp) REVERT: M 153 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8636 (mp) REVERT: M 323 MET cc_start: 0.8137 (mmm) cc_final: 0.7853 (mmm) REVERT: M 381 MET cc_start: 0.8111 (mtm) cc_final: 0.7829 (mtm) REVERT: M 398 MET cc_start: 0.7778 (tpp) cc_final: 0.7481 (tpp) REVERT: N 217 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8417 (mmtt) REVERT: N 306 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8338 (mm) REVERT: H 32 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4650 (ptp) REVERT: H 63 ASP cc_start: 0.8190 (m-30) cc_final: 0.7977 (m-30) REVERT: H 64 MET cc_start: 0.7895 (tpt) cc_final: 0.7567 (tpt) REVERT: H 73 TRP cc_start: 0.7134 (t60) cc_final: 0.6687 (t60) REVERT: H 165 MET cc_start: 0.7811 (mmt) cc_final: 0.7603 (mmp) REVERT: H 251 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8560 (mm) REVERT: A 85 LEU cc_start: 0.8553 (mt) cc_final: 0.7989 (mt) outliers start: 102 outliers final: 53 residues processed: 566 average time/residue: 0.2180 time to fit residues: 205.9319 Evaluate side-chains 530 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 470 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 293 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 44 optimal weight: 0.0970 chunk 359 optimal weight: 3.9990 chunk 255 optimal weight: 20.0000 chunk 269 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 188 optimal weight: 0.7980 chunk 400 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 HIS F 196 ASN F 341 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 867 ASN I 64 ASN I 168 ASN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.057221 restraints weight = 76838.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.058764 restraints weight = 46805.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059803 restraints weight = 33989.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.060515 restraints weight = 27409.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.060929 restraints weight = 23606.109| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37555 Z= 0.417 Angle : 2.539 50.816 51082 Z= 1.455 Chirality : 0.444 6.513 5739 Planarity : 0.005 0.096 6411 Dihedral : 5.692 89.260 5158 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.09 % Allowed : 16.00 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.00 (0.12), residues: 4629 helix: 0.95 (0.10), residues: 2606 sheet: -0.67 (0.30), residues: 314 loop : -1.32 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 804 TYR 0.018 0.001 TYR M 435 PHE 0.026 0.002 PHE L 430 TRP 0.036 0.001 TRP H 135 HIS 0.005 0.001 HIS M 241 Details of bonding type rmsd covalent geometry : bond 0.01189 (37519) covalent geometry : angle 2.21398 (50989) hydrogen bonds : bond 0.04491 ( 1654) hydrogen bonds : angle 4.14060 ( 4962) metal coordination : bond 0.03180 ( 36) metal coordination : angle 29.23202 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 477 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: F 386 GLN cc_start: 0.8647 (tt0) cc_final: 0.8380 (tt0) REVERT: E 78 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: G 308 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8847 (mp) REVERT: C 62 ASP cc_start: 0.7940 (t0) cc_final: 0.7694 (t0) REVERT: B 5 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8270 (pt) REVERT: B 170 MET cc_start: 0.8133 (mmm) cc_final: 0.7507 (mmp) REVERT: L 216 MET cc_start: 0.8039 (mtt) cc_final: 0.7663 (mtt) REVERT: L 319 MET cc_start: 0.8106 (mmt) cc_final: 0.7869 (mmt) REVERT: L 424 MET cc_start: 0.7389 (ppp) cc_final: 0.7024 (ppp) REVERT: M 145 MET cc_start: 0.6981 (tpt) cc_final: 0.6646 (tpt) REVERT: M 153 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8710 (mp) REVERT: M 323 MET cc_start: 0.8229 (mmm) cc_final: 0.7821 (mmm) REVERT: N 137 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8600 (mp) REVERT: N 255 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7801 (ttm) REVERT: H 64 MET cc_start: 0.7966 (tpt) cc_final: 0.7616 (tpt) REVERT: H 73 TRP cc_start: 0.7340 (t60) cc_final: 0.6847 (t60) REVERT: H 120 LEU cc_start: 0.9089 (mm) cc_final: 0.8765 (mp) REVERT: H 278 PHE cc_start: 0.8088 (m-80) cc_final: 0.7694 (t80) REVERT: H 286 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7692 (tpt-90) REVERT: A 85 LEU cc_start: 0.8570 (mt) cc_final: 0.8011 (mt) REVERT: J 89 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7775 (mmtt) outliers start: 118 outliers final: 78 residues processed: 562 average time/residue: 0.2173 time to fit residues: 204.3572 Evaluate side-chains 536 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 452 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 403 VAL Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 6 optimal weight: 20.0000 chunk 385 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 450 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN B 213 ASN I 168 ASN L 301 GLN L 481 GLN H 214 GLN J 86 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.070621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.057190 restraints weight = 76534.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058767 restraints weight = 45868.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.059848 restraints weight = 33163.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060568 restraints weight = 26567.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.061079 restraints weight = 22795.360| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 37555 Z= 0.404 Angle : 2.536 50.757 51082 Z= 1.453 Chirality : 0.443 6.418 5739 Planarity : 0.004 0.094 6411 Dihedral : 5.640 85.532 5156 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.51 % Allowed : 16.23 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.13 (0.12), residues: 4629 helix: 1.05 (0.10), residues: 2606 sheet: -0.65 (0.30), residues: 306 loop : -1.25 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 804 TYR 0.024 0.001 TYR M 435 PHE 0.035 0.001 PHE L 430 TRP 0.019 0.001 TRP H 135 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01168 (37519) covalent geometry : angle 2.20840 (50989) hydrogen bonds : bond 0.04322 ( 1654) hydrogen bonds : angle 4.09269 ( 4962) metal coordination : bond 0.02682 ( 36) metal coordination : angle 29.28691 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 467 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: F 386 GLN cc_start: 0.8708 (tt0) cc_final: 0.8437 (tt0) REVERT: E 78 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: G 308 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8805 (mp) REVERT: C 62 ASP cc_start: 0.7960 (t0) cc_final: 0.7701 (t0) REVERT: C 194 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5242 (ppp) REVERT: C 424 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8896 (m) REVERT: C 509 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8958 (mt) REVERT: L 127 MET cc_start: 0.8205 (tpt) cc_final: 0.7948 (tpp) REVERT: L 216 MET cc_start: 0.7919 (mtt) cc_final: 0.7597 (mtt) REVERT: L 258 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7654 (ttt) REVERT: M 153 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8657 (mp) REVERT: M 323 MET cc_start: 0.8116 (mmm) cc_final: 0.7828 (mmm) REVERT: N 137 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8520 (mp) REVERT: N 217 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8555 (mmtt) REVERT: N 255 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7801 (ttm) REVERT: H 24 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8783 (p) REVERT: H 64 MET cc_start: 0.7918 (tpt) cc_final: 0.7549 (tpt) REVERT: H 73 TRP cc_start: 0.7510 (t60) cc_final: 0.7036 (t60) REVERT: H 111 ASP cc_start: 0.7229 (t0) cc_final: 0.7022 (t0) REVERT: H 120 LEU cc_start: 0.9047 (mm) cc_final: 0.8710 (mp) REVERT: H 278 PHE cc_start: 0.8101 (m-80) cc_final: 0.7712 (t80) REVERT: A 85 LEU cc_start: 0.8525 (mt) cc_final: 0.7964 (mt) outliers start: 134 outliers final: 91 residues processed: 564 average time/residue: 0.2206 time to fit residues: 208.8986 Evaluate side-chains 549 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 447 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 641 TYR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 392 optimal weight: 6.9990 chunk 426 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS B 213 ASN L 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.055610 restraints weight = 77306.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.056513 restraints weight = 45394.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.057446 restraints weight = 35545.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.057672 restraints weight = 32613.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057776 restraints weight = 27900.830| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37555 Z= 0.444 Angle : 2.556 50.812 51082 Z= 1.461 Chirality : 0.445 6.446 5739 Planarity : 0.005 0.097 6411 Dihedral : 5.893 87.142 5156 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.85 % Allowed : 16.42 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4629 helix: 0.96 (0.10), residues: 2606 sheet: -0.64 (0.31), residues: 287 loop : -1.27 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 804 TYR 0.018 0.002 TYR L 428 PHE 0.037 0.002 PHE L 430 TRP 0.021 0.001 TRP H 135 HIS 0.006 0.001 HIS C 511 Details of bonding type rmsd covalent geometry : bond 0.01241 (37519) covalent geometry : angle 2.22963 (50989) hydrogen bonds : bond 0.04904 ( 1654) hydrogen bonds : angle 4.25702 ( 4962) metal coordination : bond 0.03295 ( 36) metal coordination : angle 29.36995 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 455 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: E 78 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: G 308 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8878 (mp) REVERT: C 194 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5624 (ppp) REVERT: C 424 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8934 (m) REVERT: C 509 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 174 GLU cc_start: 0.7596 (pt0) cc_final: 0.7340 (pt0) REVERT: B 212 THR cc_start: 0.8298 (m) cc_final: 0.8049 (p) REVERT: I 84 ASP cc_start: 0.7749 (p0) cc_final: 0.7545 (p0) REVERT: L 175 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8071 (mmm160) REVERT: L 216 MET cc_start: 0.8047 (mtt) cc_final: 0.7741 (mtt) REVERT: L 253 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9064 (mt) REVERT: L 258 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7693 (ttt) REVERT: L 430 PHE cc_start: 0.7013 (t80) cc_final: 0.6787 (t80) REVERT: L 568 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7700 (mmt) REVERT: M 153 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8665 (mp) REVERT: M 323 MET cc_start: 0.8222 (mmm) cc_final: 0.7858 (mmm) REVERT: M 381 MET cc_start: 0.8230 (mtm) cc_final: 0.7935 (mtm) REVERT: N 137 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8573 (mp) REVERT: N 217 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8633 (mmtt) REVERT: N 255 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: H 64 MET cc_start: 0.8043 (tpt) cc_final: 0.7673 (tpt) REVERT: H 120 LEU cc_start: 0.9103 (mm) cc_final: 0.8815 (mp) REVERT: H 278 PHE cc_start: 0.8307 (m-80) cc_final: 0.7903 (t80) REVERT: H 286 ARG cc_start: 0.8361 (mmm160) cc_final: 0.7955 (tpt-90) REVERT: A 85 LEU cc_start: 0.8592 (mt) cc_final: 0.8142 (mt) REVERT: J 31 TYR cc_start: 0.8868 (m-80) cc_final: 0.8520 (m-80) REVERT: J 89 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8117 (mmtt) outliers start: 147 outliers final: 96 residues processed: 563 average time/residue: 0.2264 time to fit residues: 212.5458 Evaluate side-chains 552 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 443 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 641 TYR Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 741 GLU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 304 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 282 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 338 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN L 58 GLN L 409 ASN M 206 ASN H 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.069373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056770 restraints weight = 76674.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057678 restraints weight = 42940.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058741 restraints weight = 34022.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058941 restraints weight = 30516.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.059057 restraints weight = 25879.445| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37555 Z= 0.408 Angle : 2.544 50.751 51082 Z= 1.456 Chirality : 0.443 6.416 5739 Planarity : 0.004 0.094 6411 Dihedral : 5.791 85.493 5156 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.38 % Allowed : 16.89 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 4629 helix: 1.07 (0.10), residues: 2606 sheet: -0.48 (0.32), residues: 286 loop : -1.23 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 804 TYR 0.022 0.001 TYR M 435 PHE 0.040 0.001 PHE L 430 TRP 0.019 0.001 TRP C 386 HIS 0.008 0.001 HIS M 80 Details of bonding type rmsd covalent geometry : bond 0.01175 (37519) covalent geometry : angle 2.21556 (50989) hydrogen bonds : bond 0.04529 ( 1654) hydrogen bonds : angle 4.17068 ( 4962) metal coordination : bond 0.02664 ( 36) metal coordination : angle 29.39994 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 455 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 78 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: C 62 ASP cc_start: 0.7942 (t0) cc_final: 0.7652 (t0) REVERT: C 194 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5647 (ppp) REVERT: B 174 GLU cc_start: 0.7598 (pt0) cc_final: 0.7283 (pt0) REVERT: B 178 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8270 (mtmm) REVERT: I 84 ASP cc_start: 0.7716 (p0) cc_final: 0.7477 (p0) REVERT: I 162 ASP cc_start: 0.8348 (t0) cc_final: 0.8110 (t0) REVERT: L 175 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8013 (mmm160) REVERT: L 216 MET cc_start: 0.7972 (mtt) cc_final: 0.7650 (mtt) REVERT: L 568 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7684 (mmt) REVERT: M 153 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8661 (mp) REVERT: M 323 MET cc_start: 0.8133 (mmm) cc_final: 0.7871 (mmm) REVERT: M 381 MET cc_start: 0.8216 (mtm) cc_final: 0.7937 (mtm) REVERT: M 398 MET cc_start: 0.8141 (tpp) cc_final: 0.7770 (tpp) REVERT: N 137 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8560 (mp) REVERT: N 217 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8613 (mmtt) REVERT: N 255 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7882 (tpp) REVERT: H 64 MET cc_start: 0.8009 (tpt) cc_final: 0.7712 (tpt) REVERT: H 94 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8601 (mp) REVERT: H 120 LEU cc_start: 0.9086 (mm) cc_final: 0.8773 (mp) REVERT: H 278 PHE cc_start: 0.8234 (m-80) cc_final: 0.7849 (t80) REVERT: H 286 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7982 (tpt-90) outliers start: 129 outliers final: 93 residues processed: 545 average time/residue: 0.2213 time to fit residues: 201.7012 Evaluate side-chains 541 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 438 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 641 TYR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 741 GLU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 304 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 166 optimal weight: 5.9990 chunk 197 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN L 338 HIS M 159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.058082 restraints weight = 76710.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.058724 restraints weight = 43845.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.059024 restraints weight = 36624.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.059432 restraints weight = 35047.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.059516 restraints weight = 30814.503| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37555 Z= 0.395 Angle : 2.539 50.701 51082 Z= 1.453 Chirality : 0.443 6.406 5739 Planarity : 0.004 0.092 6411 Dihedral : 5.684 85.754 5156 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.99 % Allowed : 17.41 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.28 (0.12), residues: 4629 helix: 1.17 (0.10), residues: 2602 sheet: -0.45 (0.31), residues: 286 loop : -1.19 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 160 TYR 0.026 0.001 TYR M 435 PHE 0.047 0.001 PHE L 430 TRP 0.019 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01153 (37519) covalent geometry : angle 2.20960 (50989) hydrogen bonds : bond 0.04297 ( 1654) hydrogen bonds : angle 4.10918 ( 4962) metal coordination : bond 0.02356 ( 36) metal coordination : angle 29.40504 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 455 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 78 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: C 62 ASP cc_start: 0.7951 (t0) cc_final: 0.7644 (t0) REVERT: C 424 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8896 (m) REVERT: B 152 ASP cc_start: 0.8057 (m-30) cc_final: 0.7819 (m-30) REVERT: B 174 GLU cc_start: 0.7623 (pt0) cc_final: 0.7298 (pt0) REVERT: B 178 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8244 (mtmm) REVERT: I 84 ASP cc_start: 0.7787 (p0) cc_final: 0.7512 (p0) REVERT: I 162 ASP cc_start: 0.8348 (t0) cc_final: 0.8109 (t0) REVERT: L 216 MET cc_start: 0.7950 (mtt) cc_final: 0.7636 (mtt) REVERT: L 318 TYR cc_start: 0.8393 (m-80) cc_final: 0.8144 (m-10) REVERT: L 568 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7686 (mmt) REVERT: M 124 LEU cc_start: 0.8558 (mm) cc_final: 0.8230 (mm) REVERT: M 153 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8622 (mp) REVERT: M 323 MET cc_start: 0.8060 (mmm) cc_final: 0.7853 (mmm) REVERT: N 137 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8563 (mp) REVERT: N 217 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8556 (mmtt) REVERT: N 255 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7774 (ttm) REVERT: H 64 MET cc_start: 0.7989 (tpt) cc_final: 0.7691 (tpt) REVERT: H 120 LEU cc_start: 0.9102 (mm) cc_final: 0.8833 (mp) REVERT: H 229 TYR cc_start: 0.9109 (m-80) cc_final: 0.8638 (m-10) REVERT: H 278 PHE cc_start: 0.8192 (m-80) cc_final: 0.7807 (t80) REVERT: H 286 ARG cc_start: 0.8282 (mmm160) cc_final: 0.8009 (tpt-90) REVERT: A 85 LEU cc_start: 0.8719 (mt) cc_final: 0.8458 (mt) outliers start: 114 outliers final: 82 residues processed: 539 average time/residue: 0.2246 time to fit residues: 202.2452 Evaluate side-chains 531 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 441 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 741 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 304 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 149 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 311 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN L 121 ASN L 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.054922 restraints weight = 77188.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.055689 restraints weight = 43419.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.056376 restraints weight = 34906.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.056629 restraints weight = 33200.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.056782 restraints weight = 28411.870| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.242 37555 Z= 0.458 Angle : 2.566 52.268 51082 Z= 1.465 Chirality : 0.444 6.458 5739 Planarity : 0.005 0.095 6411 Dihedral : 5.966 85.467 5156 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.46 % Allowed : 17.15 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4629 helix: 0.98 (0.10), residues: 2609 sheet: -0.50 (0.31), residues: 294 loop : -1.27 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 804 TYR 0.019 0.002 TYR L 428 PHE 0.048 0.002 PHE L 430 TRP 0.020 0.001 TRP J 87 HIS 0.007 0.001 HIS M 80 Details of bonding type rmsd covalent geometry : bond 0.01268 (37519) covalent geometry : angle 2.24013 (50989) hydrogen bonds : bond 0.05006 ( 1654) hydrogen bonds : angle 4.32876 ( 4962) metal coordination : bond 0.03272 ( 36) metal coordination : angle 29.42884 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 440 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: F 387 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8268 (mp) REVERT: E 78 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: C 62 ASP cc_start: 0.8073 (t0) cc_final: 0.7784 (t0) REVERT: C 424 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8942 (m) REVERT: B 152 ASP cc_start: 0.8093 (m-30) cc_final: 0.7848 (m-30) REVERT: B 174 GLU cc_start: 0.7620 (pt0) cc_final: 0.7332 (pt0) REVERT: B 178 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8289 (mtmm) REVERT: I 84 ASP cc_start: 0.7894 (p0) cc_final: 0.7612 (p0) REVERT: I 162 ASP cc_start: 0.8442 (t0) cc_final: 0.8225 (t0) REVERT: L 200 MET cc_start: 0.8411 (mtt) cc_final: 0.8058 (mtt) REVERT: L 216 MET cc_start: 0.8039 (mtt) cc_final: 0.7691 (mtt) REVERT: L 253 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9019 (mt) REVERT: L 318 TYR cc_start: 0.8469 (m-80) cc_final: 0.8200 (m-10) REVERT: L 568 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7788 (mmt) REVERT: M 153 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8651 (mp) REVERT: N 137 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8591 (mp) REVERT: N 217 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8650 (mmtt) REVERT: N 255 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7865 (tpp) REVERT: H 24 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8887 (p) REVERT: H 32 MET cc_start: 0.5677 (mmt) cc_final: 0.5443 (mmm) REVERT: H 64 MET cc_start: 0.7991 (tpt) cc_final: 0.7660 (tpt) REVERT: H 120 LEU cc_start: 0.9119 (mm) cc_final: 0.8847 (mp) REVERT: H 278 PHE cc_start: 0.8339 (m-80) cc_final: 0.7990 (t80) REVERT: J 31 TYR cc_start: 0.8899 (m-80) cc_final: 0.8552 (m-80) outliers start: 132 outliers final: 96 residues processed: 537 average time/residue: 0.2233 time to fit residues: 201.5987 Evaluate side-chains 537 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 430 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 741 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 304 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 274 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 269 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 319 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN L 58 GLN L 62 GLN L 121 ASN L 301 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.058096 restraints weight = 76493.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.059049 restraints weight = 43209.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.059851 restraints weight = 34325.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060113 restraints weight = 31264.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060222 restraints weight = 26666.808| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37555 Z= 0.394 Angle : 2.544 50.692 51082 Z= 1.455 Chirality : 0.442 6.401 5739 Planarity : 0.004 0.091 6411 Dihedral : 5.774 85.451 5156 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.57 % Allowed : 18.04 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4629 helix: 1.17 (0.10), residues: 2599 sheet: -0.36 (0.31), residues: 296 loop : -1.21 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 160 TYR 0.029 0.001 TYR M 435 PHE 0.050 0.001 PHE L 430 TRP 0.043 0.001 TRP H 73 HIS 0.006 0.001 HIS M 80 Details of bonding type rmsd covalent geometry : bond 0.01152 (37519) covalent geometry : angle 2.21411 (50989) hydrogen bonds : bond 0.04291 ( 1654) hydrogen bonds : angle 4.15171 ( 4962) metal coordination : bond 0.02171 ( 36) metal coordination : angle 29.46475 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 452 time to evaluate : 1.431 Fit side-chains REVERT: F 387 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8187 (mp) REVERT: E 78 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: C 62 ASP cc_start: 0.8004 (t0) cc_final: 0.7720 (t0) REVERT: C 424 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8907 (m) REVERT: B 27 ASP cc_start: 0.8432 (p0) cc_final: 0.8143 (p0) REVERT: B 66 VAL cc_start: 0.6488 (OUTLIER) cc_final: 0.6213 (t) REVERT: B 135 MET cc_start: 0.8567 (ptm) cc_final: 0.8271 (ttp) REVERT: B 152 ASP cc_start: 0.8085 (m-30) cc_final: 0.7852 (m-30) REVERT: B 174 GLU cc_start: 0.7606 (pt0) cc_final: 0.7298 (pt0) REVERT: B 178 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8259 (mtmm) REVERT: I 159 ASP cc_start: 0.5734 (p0) cc_final: 0.5372 (p0) REVERT: I 162 ASP cc_start: 0.8353 (t0) cc_final: 0.8145 (t0) REVERT: L 107 MET cc_start: 0.9038 (mmt) cc_final: 0.8703 (mmt) REVERT: L 216 MET cc_start: 0.7908 (mtt) cc_final: 0.7605 (mtt) REVERT: L 318 TYR cc_start: 0.8377 (m-80) cc_final: 0.8093 (m-10) REVERT: L 568 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7703 (mmt) REVERT: M 124 LEU cc_start: 0.8540 (mm) cc_final: 0.8226 (mm) REVERT: M 153 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8600 (mp) REVERT: M 439 MET cc_start: 0.9069 (tmm) cc_final: 0.8812 (tmm) REVERT: N 137 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8537 (mp) REVERT: N 217 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8554 (mmtt) REVERT: N 255 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7860 (tpp) REVERT: H 64 MET cc_start: 0.7952 (tpt) cc_final: 0.7635 (tpt) REVERT: H 120 LEU cc_start: 0.9093 (mm) cc_final: 0.8818 (mp) REVERT: H 229 TYR cc_start: 0.9074 (m-80) cc_final: 0.8518 (m-10) REVERT: H 278 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7868 (t80) outliers start: 98 outliers final: 73 residues processed: 522 average time/residue: 0.2258 time to fit residues: 196.6361 Evaluate side-chains 524 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 440 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 741 GLU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 512 TRP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 430 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 278 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 417 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 367 optimal weight: 20.0000 chunk 345 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 422 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN L 62 GLN L 121 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.057473 restraints weight = 76473.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.058376 restraints weight = 44221.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.059300 restraints weight = 34446.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059503 restraints weight = 31613.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.059660 restraints weight = 27081.609| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37555 Z= 0.403 Angle : 2.548 50.717 51082 Z= 1.457 Chirality : 0.443 6.394 5739 Planarity : 0.004 0.092 6411 Dihedral : 5.756 85.922 5156 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.59 % Allowed : 17.88 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.28 (0.12), residues: 4629 helix: 1.16 (0.10), residues: 2606 sheet: -0.37 (0.31), residues: 298 loop : -1.20 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 291 TYR 0.025 0.001 TYR M 435 PHE 0.044 0.001 PHE L 430 TRP 0.065 0.001 TRP H 73 HIS 0.005 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.01167 (37519) covalent geometry : angle 2.21952 (50989) hydrogen bonds : bond 0.04387 ( 1654) hydrogen bonds : angle 4.15547 ( 4962) metal coordination : bond 0.02427 ( 36) metal coordination : angle 29.39590 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6667.74 seconds wall clock time: 115 minutes 53.18 seconds (6953.18 seconds total)