Starting phenix.real_space_refine on Fri Mar 6 12:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vpz_32077/03_2026/7vpz_32077_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vpz_32077/03_2026/7vpz_32077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vpz_32077/03_2026/7vpz_32077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vpz_32077/03_2026/7vpz_32077.map" model { file = "/net/cci-nas-00/data/ceres_data/7vpz_32077/03_2026/7vpz_32077_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vpz_32077/03_2026/7vpz_32077_neut.cif" } resolution = 4.14 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= 0.002 sd= 0.040 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 Zn 8 6.06 5 P 172 5.49 5 Mg 1 5.21 5 S 100 5.16 5 C 18615 2.51 5 N 5467 2.21 5 O 6230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s 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: 30593 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1729 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "Q" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 79.658 104.045 123.886 1.00157.16 S ATOM 12691 SG CYS D 62 79.021 105.110 127.331 1.00153.61 S ATOM 12800 SG CYS D 75 82.700 103.851 126.399 1.00158.51 S ATOM 12826 SG CYS D 78 80.107 101.673 127.113 1.00149.86 S ATOM 19225 SG CYS D 886 107.733 49.258 92.669 1.00143.06 S ATOM 19789 SG CYS D 962 104.458 50.398 94.380 1.00126.36 S ATOM 19837 SG CYS D 969 105.139 51.933 90.988 1.00130.34 S ATOM 19856 SG CYS D 972 104.370 48.451 91.235 1.00129.45 S ATOM 25721 SG CYS M 90 77.896 161.190 48.514 1.00387.00 S ATOM 25743 SG CYS M 93 75.646 163.050 51.006 1.00382.83 S ATOM 26016 SG CYS M 130 74.193 160.628 48.385 1.00381.94 S ATOM 26035 SG CYS M 133 75.630 164.092 47.445 1.00371.66 S ATOM 25635 SG CYS M 79 79.644 148.248 57.441 1.00382.76 S ATOM 26705 SG CYS N 90 101.327 136.404 43.201 1.00397.98 S ATOM 26727 SG CYS N 93 104.918 135.407 42.086 1.00401.09 S ATOM 27000 SG CYS N 130 101.758 133.887 40.505 1.00399.20 S ATOM 27019 SG CYS N 133 102.929 133.002 44.039 1.00395.05 S ATOM 26619 SG CYS N 79 98.195 147.250 32.369 1.00384.58 S Time building chain proxies: 6.69, per 1000 atoms: 0.22 Number of scatterers: 30593 At special positions: 0 Unit cell: (136.4, 202.4, 209, 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) Zn 8 29.99 S 100 16.00 P 172 15.00 Mg 1 11.99 O 6230 8.00 N 5467 7.00 C 18615 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 24 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6402 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 43 sheets defined 44.1% alpha, 13.9% beta 65 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.004A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.685A pdb=" N LEU B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.504A pdb=" N THR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.593A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.544A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.518A pdb=" N GLY C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.959A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.596A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.051A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 568 through 573 removed outlier: 4.656A pdb=" N MET C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 580 removed outlier: 4.111A pdb=" N ILE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 587 through 598 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 716 through 720 removed outlier: 4.178A pdb=" N ASP C 719 " --> pdb=" O ASN C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 764 through 768 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 911 removed outlier: 4.201A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.605A pdb=" N LEU C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 Processing helix chain 'C' and resid 1021 through 1026 Processing helix chain 'C' and resid 1054 through 1065 Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.517A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.101A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.910A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.771A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 227 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.547A pdb=" N ALA D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.591A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.582A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 360 removed outlier: 4.047A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.515A pdb=" N LEU D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.594A pdb=" N GLN D 415 " --> pdb=" O GLY D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.474A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.537A pdb=" N PHE D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 662 through 672 Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 4.157A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.536A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.649A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 876 removed outlier: 3.843A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.889A pdb=" N SER D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 970 through 974 Processing helix chain 'D' and resid 988 through 999 removed outlier: 4.102A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.300A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 4.000A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.126A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 Processing helix chain 'D' and resid 1212 through 1223 Processing helix chain 'D' and resid 1231 through 1238 Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.670A pdb=" N LYS D1262 " --> pdb=" O THR D1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 removed outlier: 4.350A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.637A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.872A pdb=" N ASP F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 282 Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.719A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 346 " --> pdb=" O MET F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 476 Processing helix chain 'F' and resid 482 through 498 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.953A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.510A pdb=" N VAL M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.928A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 removed outlier: 3.529A pdb=" N ALA M 134 " --> pdb=" O CYS M 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.223A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.146A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 5.486A pdb=" N GLU A 11 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 22 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 13 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 20 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 8.019A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.770A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.889A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR B 175 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.502A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 50 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.618A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 105 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.666A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.516A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY C 613 " --> pdb=" O VAL C 957 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 6.682A pdb=" N THR C 124 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS C 98 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE C 122 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C 100 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN C 129 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 134 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.608A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 440 through 442 removed outlier: 3.707A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.656A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.712A pdb=" N ASP C 566 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 628 through 629 removed outlier: 7.005A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 634 through 639 removed outlier: 3.561A pdb=" N THR C 647 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC5, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.527A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 734 through 746 removed outlier: 5.700A pdb=" N SER C 735 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 862 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS C 737 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 860 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU C 739 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR C 858 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS C 741 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARG C 856 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 743 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU C 854 " --> pdb=" O VAL C 743 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 745 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN C 852 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP C 840 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 854 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 838 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG C 856 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 836 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 858 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 862 " --> pdb=" O ILE C 830 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N ILE C 830 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AC8, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.614A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1027 through 1029 Processing sheet with id=AD2, first strand: chain 'C' and resid 1121 through 1123 removed outlier: 3.581A pdb=" N LEU D 10 " --> pdb=" O ASP D1226 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.411A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.623A pdb=" N THR D 337 " --> pdb=" O ILE F 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 566 through 567 removed outlier: 4.098A pdb=" N ARG D 572 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD9, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AE1, first strand: chain 'D' and resid 892 through 894 removed outlier: 4.112A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.533A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE4, first strand: chain 'D' and resid 1254 through 1256 removed outlier: 3.585A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D1256 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR E 81 " --> pdb=" O GLU D1256 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AE6, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.439A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS N 87 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 30 through 31 1241 hydrogen bonds defined for protein. 3522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 173 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9417 1.34 - 1.46: 5296 1.46 - 1.58: 16223 1.58 - 1.70: 342 1.70 - 1.82: 175 Bond restraints: 31453 Sorted by residual: bond pdb=" CA GLN C1040 " pdb=" C GLN C1040 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" O3' DG O 71 " pdb=" P DG O 72 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" C1' DG P 15 " pdb=" N9 DG P 15 " ideal model delta sigma weight residual 1.460 1.402 0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.81e+00 bond pdb=" N ALA D 133 " pdb=" CA ALA D 133 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.44e+00 ... (remaining 31448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 42666 2.75 - 5.50: 584 5.50 - 8.25: 34 8.25 - 10.99: 8 10.99 - 13.74: 1 Bond angle restraints: 43293 Sorted by residual: angle pdb=" N GLY D 286 " pdb=" CA GLY D 286 " pdb=" C GLY D 286 " ideal model delta sigma weight residual 111.80 125.54 -13.74 1.82e+00 3.02e-01 5.70e+01 angle pdb=" N MET C1036 " pdb=" CA MET C1036 " pdb=" C MET C1036 " ideal model delta sigma weight residual 111.14 118.91 -7.77 1.08e+00 8.57e-01 5.18e+01 angle pdb=" N TYR D 134 " pdb=" CA TYR D 134 " pdb=" C TYR D 134 " ideal model delta sigma weight residual 110.55 119.65 -9.10 1.35e+00 5.49e-01 4.54e+01 angle pdb=" N TYR D 130 " pdb=" CA TYR D 130 " pdb=" C TYR D 130 " ideal model delta sigma weight residual 109.96 100.07 9.89 1.50e+00 4.44e-01 4.35e+01 angle pdb=" N ALA C 872 " pdb=" CA ALA C 872 " pdb=" C ALA C 872 " ideal model delta sigma weight residual 108.55 117.44 -8.89 1.62e+00 3.81e-01 3.01e+01 ... (remaining 43288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 17809 35.45 - 70.89: 888 70.89 - 106.34: 30 106.34 - 141.78: 4 141.78 - 177.23: 14 Dihedral angle restraints: 18745 sinusoidal: 8799 harmonic: 9946 Sorted by residual: dihedral pdb=" C LYS D 823 " pdb=" N LYS D 823 " pdb=" CA LYS D 823 " pdb=" CB LYS D 823 " ideal model delta harmonic sigma weight residual -122.60 -135.45 12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N LYS D 823 " pdb=" C LYS D 823 " pdb=" CA LYS D 823 " pdb=" CB LYS D 823 " ideal model delta harmonic sigma weight residual 122.80 135.62 -12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" CA ALA C 907 " pdb=" C ALA C 907 " pdb=" N VAL C 908 " pdb=" CA VAL C 908 " ideal model delta harmonic sigma weight residual 180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 18742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4637 0.098 - 0.196: 264 0.196 - 0.294: 19 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 4923 Sorted by residual: chirality pdb=" CA LYS D 823 " pdb=" N LYS D 823 " pdb=" C LYS D 823 " pdb=" CB LYS D 823 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA GLN C1039 " pdb=" N GLN C1039 " pdb=" C GLN C1039 " pdb=" CB GLN C1039 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ARG C 293 " pdb=" N ARG C 293 " pdb=" C ARG C 293 " pdb=" CB ARG C 293 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 4920 not shown) Planarity restraints: 5067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 443 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO D 444 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 444 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 444 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1059 " 0.009 2.00e-02 2.50e+03 1.51e-02 5.74e+00 pdb=" CG TRP C1059 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C1059 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C1059 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C1059 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1059 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1059 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1059 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1059 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1059 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 738 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LYS D 738 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS D 738 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 739 " 0.013 2.00e-02 2.50e+03 ... (remaining 5064 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 202 2.49 - 3.09: 23379 3.09 - 3.69: 50724 3.69 - 4.30: 69675 4.30 - 4.90: 108837 Nonbonded interactions: 252817 Sorted by model distance: nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.887 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.903 2.230 nonbonded pdb=" O3' G Q 5 " pdb="MG MG D1401 " model vdw 1.974 2.170 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.066 2.230 nonbonded pdb=" OG1 THR C 339 " pdb=" OE1 GLU C 340 " model vdw 2.107 3.040 ... (remaining 252812 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.880 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31481 Z= 0.228 Angle : 0.798 13.742 43317 Z= 0.459 Chirality : 0.049 0.490 4923 Planarity : 0.005 0.063 5067 Dihedral : 18.738 177.230 12343 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.52 % Allowed : 1.31 % Favored : 98.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3458 helix: 1.09 (0.14), residues: 1372 sheet: -0.82 (0.25), residues: 401 loop : -0.68 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 22 TYR 0.026 0.002 TYR E 32 PHE 0.022 0.002 PHE B 219 TRP 0.038 0.002 TRP C1059 HIS 0.018 0.001 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00461 (31453) covalent geometry : angle 0.78565 (43293) hydrogen bonds : bond 0.14747 ( 1408) hydrogen bonds : angle 5.98346 ( 3864) metal coordination : bond 0.00556 ( 28) metal coordination : angle 5.95049 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 543 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9134 (pptt) cc_final: 0.8784 (ptpp) REVERT: A 95 MET cc_start: 0.8532 (ttm) cc_final: 0.8185 (ttm) REVERT: A 153 LYS cc_start: 0.8252 (pttp) cc_final: 0.7570 (tptt) REVERT: B 5 GLN cc_start: 0.7335 (mp10) cc_final: 0.6899 (mp10) REVERT: B 150 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7705 (m) REVERT: C 76 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9029 (tm-30) REVERT: C 269 LEU cc_start: 0.9114 (mm) cc_final: 0.8652 (tp) REVERT: C 383 GLU cc_start: 0.8485 (tt0) cc_final: 0.8234 (mt-10) REVERT: C 438 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8472 (mmtt) REVERT: C 725 GLN cc_start: 0.6764 (tm-30) cc_final: 0.6383 (tm-30) REVERT: D 19 ASP cc_start: 0.8431 (t0) cc_final: 0.8175 (t70) REVERT: D 154 HIS cc_start: 0.9428 (m90) cc_final: 0.9118 (m-70) REVERT: D 296 LEU cc_start: 0.9150 (mt) cc_final: 0.8542 (mt) REVERT: D 356 ARG cc_start: 0.8272 (tpm170) cc_final: 0.8066 (tpm170) REVERT: D 457 MET cc_start: 0.7977 (ttp) cc_final: 0.7766 (ttm) REVERT: D 470 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9233 (mmtm) REVERT: D 831 ILE cc_start: 0.9419 (mt) cc_final: 0.9012 (mt) REVERT: D 843 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8100 (mt-10) REVERT: D 881 ILE cc_start: 0.7734 (mm) cc_final: 0.7513 (mm) REVERT: D 919 MET cc_start: 0.6382 (mmm) cc_final: 0.4875 (mmp) REVERT: D 971 MET cc_start: 0.8134 (mmm) cc_final: 0.7890 (tpp) REVERT: D 1143 GLN cc_start: 0.8868 (tp40) cc_final: 0.8666 (tp40) REVERT: D 1191 MET cc_start: 0.7748 (pmm) cc_final: 0.7524 (pmm) REVERT: E 18 GLU cc_start: 0.8576 (mp0) cc_final: 0.8358 (pm20) REVERT: E 26 LYS cc_start: 0.8481 (mttt) cc_final: 0.7839 (mmmm) REVERT: E 70 ILE cc_start: 0.8844 (mp) cc_final: 0.8569 (mp) REVERT: E 75 ILE cc_start: 0.8366 (mm) cc_final: 0.8135 (mm) REVERT: F 324 TYR cc_start: 0.8104 (m-80) cc_final: 0.7802 (m-80) outliers start: 15 outliers final: 1 residues processed: 553 average time/residue: 0.2262 time to fit residues: 192.4071 Evaluate side-chains 395 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN B 185 GLN C 220 GLN C 374 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 HIS D 103 HIS D 307 ASN ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.135945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097218 restraints weight = 108340.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098769 restraints weight = 72953.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.100024 restraints weight = 50889.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.100222 restraints weight = 41649.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100277 restraints weight = 37541.339| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31481 Z= 0.161 Angle : 0.653 9.996 43317 Z= 0.349 Chirality : 0.043 0.215 4923 Planarity : 0.005 0.072 5067 Dihedral : 20.958 178.679 5662 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3458 helix: 1.07 (0.13), residues: 1402 sheet: -0.76 (0.25), residues: 400 loop : -0.53 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 247 TYR 0.022 0.001 TYR E 32 PHE 0.050 0.002 PHE D1209 TRP 0.021 0.002 TRP D1203 HIS 0.005 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00360 (31453) covalent geometry : angle 0.64278 (43293) hydrogen bonds : bond 0.04987 ( 1408) hydrogen bonds : angle 4.76768 ( 3864) metal coordination : bond 0.00472 ( 28) metal coordination : angle 4.84125 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 507 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9170 (pptt) cc_final: 0.8780 (ptpp) REVERT: B 5 GLN cc_start: 0.7362 (mp10) cc_final: 0.6941 (mp10) REVERT: B 152 ASN cc_start: 0.7516 (m-40) cc_final: 0.7277 (m-40) REVERT: C 76 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8779 (tm-30) REVERT: C 193 ILE cc_start: 0.8611 (tp) cc_final: 0.8274 (tp) REVERT: C 201 GLU cc_start: 0.6840 (mp0) cc_final: 0.6604 (mp0) REVERT: C 382 MET cc_start: 0.9056 (tmm) cc_final: 0.8567 (tmm) REVERT: C 383 GLU cc_start: 0.8484 (tt0) cc_final: 0.8255 (mt-10) REVERT: C 438 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8391 (mmtt) REVERT: C 473 GLU cc_start: 0.7867 (pt0) cc_final: 0.7510 (pt0) REVERT: C 593 MET cc_start: 0.7786 (mmm) cc_final: 0.7562 (mmm) REVERT: C 725 GLN cc_start: 0.6847 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 839 PHE cc_start: 0.7131 (m-10) cc_final: 0.6653 (m-10) REVERT: C 1018 LEU cc_start: 0.9200 (mp) cc_final: 0.8981 (mp) REVERT: C 1053 PHE cc_start: 0.6477 (t80) cc_final: 0.6138 (t80) REVERT: C 1119 ASN cc_start: 0.6555 (p0) cc_final: 0.6318 (t0) REVERT: D 19 ASP cc_start: 0.8389 (t0) cc_final: 0.8138 (t0) REVERT: D 154 HIS cc_start: 0.9345 (m90) cc_final: 0.9059 (m90) REVERT: D 241 TYR cc_start: 0.8484 (t80) cc_final: 0.8271 (t80) REVERT: D 252 PHE cc_start: 0.8412 (p90) cc_final: 0.7409 (p90) REVERT: D 264 ARG cc_start: 0.8492 (tpm170) cc_final: 0.8258 (tpm170) REVERT: D 296 LEU cc_start: 0.9230 (mt) cc_final: 0.8798 (mt) REVERT: D 373 MET cc_start: 0.7559 (tpp) cc_final: 0.6694 (tpp) REVERT: D 470 LYS cc_start: 0.9428 (mmmm) cc_final: 0.9155 (mmtm) REVERT: D 475 MET cc_start: 0.8974 (tpt) cc_final: 0.8722 (tpt) REVERT: D 831 ILE cc_start: 0.9300 (mt) cc_final: 0.8887 (mt) REVERT: D 843 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8074 (mt-10) REVERT: D 881 ILE cc_start: 0.7678 (mm) cc_final: 0.7385 (mm) REVERT: D 919 MET cc_start: 0.7135 (mmm) cc_final: 0.6903 (mmp) REVERT: E 60 ASP cc_start: 0.8255 (p0) cc_final: 0.7943 (p0) REVERT: E 70 ILE cc_start: 0.8686 (mp) cc_final: 0.8436 (mp) REVERT: F 229 ASN cc_start: 0.8836 (t0) cc_final: 0.8358 (p0) REVERT: F 342 MET cc_start: 0.7656 (ppp) cc_final: 0.7158 (ppp) REVERT: F 422 ILE cc_start: 0.8068 (tp) cc_final: 0.7863 (tp) outliers start: 3 outliers final: 0 residues processed: 510 average time/residue: 0.2197 time to fit residues: 173.0084 Evaluate side-chains 373 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 227 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 170 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 248 optimal weight: 0.0980 chunk 182 optimal weight: 0.0070 chunk 342 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 330 optimal weight: 40.0000 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 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 = 0.4326 r_free = 0.4326 target = 0.137342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098425 restraints weight = 108982.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099408 restraints weight = 75828.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100618 restraints weight = 56911.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101703 restraints weight = 42047.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.101498 restraints weight = 38509.189| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31481 Z= 0.136 Angle : 0.623 13.326 43317 Z= 0.329 Chirality : 0.042 0.189 4923 Planarity : 0.004 0.062 5067 Dihedral : 20.894 179.584 5662 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3458 helix: 1.03 (0.13), residues: 1403 sheet: -0.53 (0.25), residues: 405 loop : -0.49 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1147 TYR 0.034 0.001 TYR E 32 PHE 0.030 0.002 PHE D1209 TRP 0.032 0.002 TRP C 924 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00298 (31453) covalent geometry : angle 0.61249 (43293) hydrogen bonds : bond 0.04290 ( 1408) hydrogen bonds : angle 4.51140 ( 3864) metal coordination : bond 0.00412 ( 28) metal coordination : angle 4.98063 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9046 (pptt) cc_final: 0.8791 (ptpt) REVERT: A 202 MET cc_start: 0.8484 (pmm) cc_final: 0.8110 (pmm) REVERT: B 5 GLN cc_start: 0.7410 (mp10) cc_final: 0.6914 (mp10) REVERT: B 152 ASN cc_start: 0.7534 (m-40) cc_final: 0.7260 (m-40) REVERT: C 76 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8732 (tm-30) REVERT: C 356 ILE cc_start: 0.9040 (pt) cc_final: 0.8748 (pt) REVERT: C 382 MET cc_start: 0.9060 (tmm) cc_final: 0.8636 (tmm) REVERT: C 383 GLU cc_start: 0.8470 (tt0) cc_final: 0.8263 (mt-10) REVERT: C 473 GLU cc_start: 0.7692 (pt0) cc_final: 0.7483 (pt0) REVERT: C 587 ASP cc_start: 0.8292 (t70) cc_final: 0.8062 (t70) REVERT: C 593 MET cc_start: 0.7840 (mmm) cc_final: 0.7590 (mmm) REVERT: C 701 LEU cc_start: 0.8372 (mp) cc_final: 0.7979 (mp) REVERT: C 718 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7621 (tp30) REVERT: C 723 LEU cc_start: 0.8986 (pp) cc_final: 0.8694 (pt) REVERT: C 725 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 1018 LEU cc_start: 0.9180 (mp) cc_final: 0.8950 (mp) REVERT: C 1053 PHE cc_start: 0.6590 (t80) cc_final: 0.6257 (t80) REVERT: C 1118 LEU cc_start: 0.8592 (mp) cc_final: 0.8291 (mp) REVERT: C 1119 ASN cc_start: 0.6590 (p0) cc_final: 0.6166 (t0) REVERT: D 19 ASP cc_start: 0.8308 (t0) cc_final: 0.8017 (t0) REVERT: D 29 LYS cc_start: 0.8846 (ptpp) cc_final: 0.8579 (mtmm) REVERT: D 103 HIS cc_start: 0.6314 (t70) cc_final: 0.5907 (t70) REVERT: D 154 HIS cc_start: 0.9333 (m90) cc_final: 0.9029 (m90) REVERT: D 264 ARG cc_start: 0.8543 (tpm170) cc_final: 0.8256 (tpm170) REVERT: D 296 LEU cc_start: 0.9154 (mt) cc_final: 0.8694 (mt) REVERT: D 314 LEU cc_start: 0.8284 (pt) cc_final: 0.8066 (pt) REVERT: D 373 MET cc_start: 0.7500 (tpp) cc_final: 0.6847 (tpp) REVERT: D 428 SER cc_start: 0.9438 (m) cc_final: 0.9237 (m) REVERT: D 475 MET cc_start: 0.9096 (tpt) cc_final: 0.8841 (tpt) REVERT: D 721 ARG cc_start: 0.6872 (tpp80) cc_final: 0.6256 (tpp80) REVERT: D 807 MET cc_start: 0.8788 (pmm) cc_final: 0.8440 (pmm) REVERT: D 808 GLN cc_start: 0.8892 (mp10) cc_final: 0.8359 (mp10) REVERT: D 831 ILE cc_start: 0.9249 (mt) cc_final: 0.8922 (mt) REVERT: D 843 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8130 (mt-10) REVERT: D 919 MET cc_start: 0.6888 (mmm) cc_final: 0.6602 (mmp) REVERT: F 229 ASN cc_start: 0.8817 (t0) cc_final: 0.8379 (p0) REVERT: F 311 LEU cc_start: 0.8470 (tt) cc_final: 0.8169 (tt) REVERT: F 334 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.2975 (mt) REVERT: F 342 MET cc_start: 0.7614 (ppp) cc_final: 0.7177 (ppp) REVERT: F 420 ASP cc_start: 0.8435 (m-30) cc_final: 0.8166 (m-30) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.2021 time to fit residues: 160.5617 Evaluate side-chains 377 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 332 optimal weight: 40.0000 chunk 144 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 205 optimal weight: 0.0670 chunk 82 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN C 374 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 HIS ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 778 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1182 HIS ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.132029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094398 restraints weight = 110417.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093726 restraints weight = 72823.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094553 restraints weight = 59403.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094773 restraints weight = 52648.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094962 restraints weight = 46181.903| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31481 Z= 0.214 Angle : 0.675 12.481 43317 Z= 0.359 Chirality : 0.043 0.198 4923 Planarity : 0.005 0.065 5067 Dihedral : 20.863 179.598 5662 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3458 helix: 0.87 (0.14), residues: 1398 sheet: -0.63 (0.24), residues: 425 loop : -0.61 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 347 TYR 0.022 0.002 TYR C 717 PHE 0.036 0.002 PHE D1209 TRP 0.029 0.002 TRP C 924 HIS 0.006 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00476 (31453) covalent geometry : angle 0.66390 (43293) hydrogen bonds : bond 0.04539 ( 1408) hydrogen bonds : angle 4.62093 ( 3864) metal coordination : bond 0.00942 ( 28) metal coordination : angle 5.14883 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9171 (pptt) cc_final: 0.8734 (ptpp) REVERT: B 152 ASN cc_start: 0.7573 (m-40) cc_final: 0.7363 (m110) REVERT: B 202 MET cc_start: 0.8051 (mtt) cc_final: 0.7796 (mtm) REVERT: C 76 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8793 (tm-30) REVERT: C 269 LEU cc_start: 0.9201 (mm) cc_final: 0.8825 (tp) REVERT: C 356 ILE cc_start: 0.9210 (pt) cc_final: 0.8930 (pt) REVERT: C 362 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7650 (mtt-85) REVERT: C 382 MET cc_start: 0.9040 (tmm) cc_final: 0.8793 (tmm) REVERT: C 429 ASN cc_start: 0.8403 (m-40) cc_final: 0.8123 (m-40) REVERT: C 593 MET cc_start: 0.7892 (mmm) cc_final: 0.7619 (mmm) REVERT: C 710 MET cc_start: 0.8548 (ppp) cc_final: 0.8300 (ppp) REVERT: C 725 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6556 (tm-30) REVERT: C 1018 LEU cc_start: 0.9266 (mp) cc_final: 0.8998 (mp) REVERT: C 1119 ASN cc_start: 0.6828 (p0) cc_final: 0.6565 (t0) REVERT: D 19 ASP cc_start: 0.8490 (t0) cc_final: 0.8211 (t70) REVERT: D 29 LYS cc_start: 0.8812 (ptpp) cc_final: 0.8558 (mtmm) REVERT: D 103 HIS cc_start: 0.6980 (t70) cc_final: 0.6428 (t70) REVERT: D 154 HIS cc_start: 0.9431 (m90) cc_final: 0.9053 (m90) REVERT: D 264 ARG cc_start: 0.8653 (tpm170) cc_final: 0.8331 (tpm170) REVERT: D 296 LEU cc_start: 0.9297 (mt) cc_final: 0.8782 (mt) REVERT: D 356 ARG cc_start: 0.8253 (tpm170) cc_final: 0.7964 (tpm170) REVERT: D 373 MET cc_start: 0.7873 (tpp) cc_final: 0.7470 (tpp) REVERT: D 475 MET cc_start: 0.9228 (tpt) cc_final: 0.8961 (tpt) REVERT: D 560 LEU cc_start: 0.8980 (tp) cc_final: 0.8776 (tp) REVERT: D 843 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8098 (mt-10) REVERT: F 229 ASN cc_start: 0.8799 (t0) cc_final: 0.8387 (p0) REVERT: F 298 MET cc_start: 0.6917 (ttp) cc_final: 0.6659 (ttp) REVERT: F 342 MET cc_start: 0.7705 (ppp) cc_final: 0.7336 (ppp) REVERT: F 355 MET cc_start: 0.8307 (tpt) cc_final: 0.7820 (tpp) REVERT: F 422 ILE cc_start: 0.8226 (tp) cc_final: 0.7971 (tp) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.2009 time to fit residues: 143.8983 Evaluate side-chains 342 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 61 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 100 optimal weight: 0.4980 chunk 241 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 200 GLN B 151 GLN C 374 GLN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.133743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096170 restraints weight = 110430.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096248 restraints weight = 72729.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.096758 restraints weight = 54588.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097196 restraints weight = 51851.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097329 restraints weight = 44579.824| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31481 Z= 0.144 Angle : 0.614 14.633 43317 Z= 0.324 Chirality : 0.042 0.204 4923 Planarity : 0.004 0.050 5067 Dihedral : 20.790 179.990 5662 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3458 helix: 0.93 (0.14), residues: 1404 sheet: -0.59 (0.24), residues: 416 loop : -0.54 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 84 TYR 0.023 0.002 TYR C1014 PHE 0.029 0.002 PHE A 30 TRP 0.030 0.002 TRP C 924 HIS 0.005 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00323 (31453) covalent geometry : angle 0.60085 (43293) hydrogen bonds : bond 0.04068 ( 1408) hydrogen bonds : angle 4.41473 ( 3864) metal coordination : bond 0.00597 ( 28) metal coordination : angle 5.38724 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9172 (pptt) cc_final: 0.8719 (ptpp) REVERT: A 202 MET cc_start: 0.8430 (pmm) cc_final: 0.8102 (pmm) REVERT: B 5 GLN cc_start: 0.7965 (mp10) cc_final: 0.7657 (mp10) REVERT: B 82 GLN cc_start: 0.8353 (tt0) cc_final: 0.7675 (pt0) REVERT: B 202 MET cc_start: 0.8258 (mtt) cc_final: 0.8000 (mtm) REVERT: C 76 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8749 (tm-30) REVERT: C 148 MET cc_start: 0.8627 (tpt) cc_final: 0.8333 (tpt) REVERT: C 201 GLU cc_start: 0.6774 (mp0) cc_final: 0.6424 (mp0) REVERT: C 356 ILE cc_start: 0.9225 (pt) cc_final: 0.8837 (pt) REVERT: C 362 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7470 (mtt-85) REVERT: C 382 MET cc_start: 0.9049 (tmm) cc_final: 0.8700 (tmm) REVERT: C 383 GLU cc_start: 0.8331 (tt0) cc_final: 0.7887 (mt-10) REVERT: C 429 ASN cc_start: 0.8546 (m-40) cc_final: 0.8178 (m-40) REVERT: C 587 ASP cc_start: 0.8741 (t0) cc_final: 0.8441 (t70) REVERT: C 710 MET cc_start: 0.8451 (ppp) cc_final: 0.8129 (ppp) REVERT: C 1018 LEU cc_start: 0.9195 (mp) cc_final: 0.8991 (mp) REVERT: C 1053 PHE cc_start: 0.7166 (t80) cc_final: 0.6691 (t80) REVERT: D 19 ASP cc_start: 0.8417 (t0) cc_final: 0.8108 (t70) REVERT: D 29 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8655 (pttt) REVERT: D 103 HIS cc_start: 0.6833 (t70) cc_final: 0.6622 (t70) REVERT: D 154 HIS cc_start: 0.9391 (m90) cc_final: 0.9034 (m90) REVERT: D 264 ARG cc_start: 0.8565 (tpm170) cc_final: 0.8221 (tpm170) REVERT: D 296 LEU cc_start: 0.9299 (mt) cc_final: 0.8776 (mt) REVERT: D 356 ARG cc_start: 0.8354 (tpm170) cc_final: 0.8011 (tpm170) REVERT: D 405 MET cc_start: 0.8104 (tpp) cc_final: 0.7741 (tpp) REVERT: D 475 MET cc_start: 0.9271 (tpt) cc_final: 0.8942 (tpt) REVERT: D 808 GLN cc_start: 0.8911 (mp10) cc_final: 0.8390 (mp10) REVERT: D 843 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 919 MET cc_start: 0.7034 (mmm) cc_final: 0.6606 (mmm) REVERT: F 229 ASN cc_start: 0.8819 (t0) cc_final: 0.8497 (p0) REVERT: F 298 MET cc_start: 0.6819 (ttp) cc_final: 0.6454 (ttp) REVERT: F 342 MET cc_start: 0.7608 (ppp) cc_final: 0.7219 (ppp) REVERT: F 355 MET cc_start: 0.8325 (tpt) cc_final: 0.7849 (tpp) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.2061 time to fit residues: 152.6997 Evaluate side-chains 347 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 259 optimal weight: 0.2980 chunk 232 optimal weight: 0.6980 chunk 330 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 337 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 326 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 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 = 0.4257 r_free = 0.4257 target = 0.132100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093913 restraints weight = 110902.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093979 restraints weight = 77007.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095212 restraints weight = 58231.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095292 restraints weight = 49825.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095320 restraints weight = 44296.698| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31481 Z= 0.172 Angle : 0.630 13.825 43317 Z= 0.333 Chirality : 0.042 0.274 4923 Planarity : 0.004 0.060 5067 Dihedral : 20.737 179.239 5662 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3458 helix: 0.87 (0.14), residues: 1400 sheet: -0.77 (0.23), residues: 439 loop : -0.56 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 407 TYR 0.030 0.002 TYR E 32 PHE 0.045 0.002 PHE A 189 TRP 0.033 0.002 TRP C 924 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00388 (31453) covalent geometry : angle 0.61806 (43293) hydrogen bonds : bond 0.04105 ( 1408) hydrogen bonds : angle 4.46689 ( 3864) metal coordination : bond 0.00666 ( 28) metal coordination : angle 5.20778 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8786 (ptmm) cc_final: 0.8513 (ptmm) REVERT: A 202 MET cc_start: 0.8538 (pmm) cc_final: 0.8198 (pmm) REVERT: B 5 GLN cc_start: 0.7984 (mp10) cc_final: 0.7677 (mp10) REVERT: B 82 GLN cc_start: 0.8425 (tt0) cc_final: 0.7761 (pt0) REVERT: B 202 MET cc_start: 0.8369 (mtt) cc_final: 0.8155 (mtm) REVERT: C 76 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8818 (tm-30) REVERT: C 148 MET cc_start: 0.8606 (tpt) cc_final: 0.8262 (tpt) REVERT: C 209 MET cc_start: 0.7110 (mmp) cc_final: 0.6894 (mmp) REVERT: C 382 MET cc_start: 0.9077 (tmm) cc_final: 0.8762 (tmm) REVERT: C 429 ASN cc_start: 0.8510 (m-40) cc_final: 0.8208 (m-40) REVERT: C 710 MET cc_start: 0.8544 (ppp) cc_final: 0.8271 (ppp) REVERT: C 992 LYS cc_start: 0.8041 (mttm) cc_final: 0.7690 (mttm) REVERT: D 19 ASP cc_start: 0.8479 (t0) cc_final: 0.8251 (t70) REVERT: D 29 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8626 (pttt) REVERT: D 30 LYS cc_start: 0.9045 (tptm) cc_final: 0.8771 (tptm) REVERT: D 103 HIS cc_start: 0.6661 (t70) cc_final: 0.6329 (t70) REVERT: D 264 ARG cc_start: 0.8603 (tpm170) cc_final: 0.8152 (tpm170) REVERT: D 296 LEU cc_start: 0.9325 (mt) cc_final: 0.8843 (mt) REVERT: D 314 LEU cc_start: 0.8404 (pt) cc_final: 0.8199 (pt) REVERT: D 356 ARG cc_start: 0.8348 (tpm170) cc_final: 0.8111 (tpm170) REVERT: D 373 MET cc_start: 0.7783 (tpp) cc_final: 0.7438 (tpp) REVERT: D 405 MET cc_start: 0.8094 (tpp) cc_final: 0.7748 (tpp) REVERT: D 590 THR cc_start: 0.6564 (m) cc_final: 0.6337 (m) REVERT: D 831 ILE cc_start: 0.9353 (mt) cc_final: 0.9097 (mt) REVERT: D 919 MET cc_start: 0.6983 (mmm) cc_final: 0.6448 (mmm) REVERT: D 971 MET cc_start: 0.8355 (ppp) cc_final: 0.8133 (ppp) REVERT: E 79 LEU cc_start: 0.8456 (mp) cc_final: 0.7920 (tt) REVERT: F 229 ASN cc_start: 0.8825 (t0) cc_final: 0.8437 (p0) REVERT: F 298 MET cc_start: 0.6985 (ttp) cc_final: 0.6564 (ttt) REVERT: F 342 MET cc_start: 0.7731 (ppp) cc_final: 0.7296 (ppp) REVERT: F 355 MET cc_start: 0.8353 (tpt) cc_final: 0.7871 (tpp) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.2049 time to fit residues: 145.7027 Evaluate side-chains 343 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 86 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 247 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 314 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 12 optimal weight: 10.0000 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1189 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.134128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096127 restraints weight = 109978.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096233 restraints weight = 76842.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097526 restraints weight = 57277.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.097643 restraints weight = 48743.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097817 restraints weight = 44246.093| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31481 Z= 0.129 Angle : 0.631 12.026 43317 Z= 0.329 Chirality : 0.042 0.231 4923 Planarity : 0.004 0.065 5067 Dihedral : 20.687 178.887 5662 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.03 % Allowed : 1.48 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3458 helix: 0.97 (0.14), residues: 1393 sheet: -0.59 (0.24), residues: 428 loop : -0.50 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG D 810 TYR 0.028 0.001 TYR E 32 PHE 0.022 0.002 PHE A 30 TRP 0.034 0.002 TRP C 924 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00287 (31453) covalent geometry : angle 0.61946 (43293) hydrogen bonds : bond 0.03936 ( 1408) hydrogen bonds : angle 4.31778 ( 3864) metal coordination : bond 0.00409 ( 28) metal coordination : angle 5.16594 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8805 (ptmm) cc_final: 0.8527 (ptmm) REVERT: A 202 MET cc_start: 0.8531 (pmm) cc_final: 0.8137 (pmm) REVERT: B 5 GLN cc_start: 0.7964 (mp10) cc_final: 0.7720 (mp10) REVERT: B 82 GLN cc_start: 0.8407 (tt0) cc_final: 0.7695 (pt0) REVERT: B 202 MET cc_start: 0.8320 (mtt) cc_final: 0.8089 (mtm) REVERT: C 148 MET cc_start: 0.8529 (tpt) cc_final: 0.8158 (tpt) REVERT: C 356 ILE cc_start: 0.9256 (pt) cc_final: 0.9001 (pt) REVERT: C 362 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7540 (mtt-85) REVERT: C 382 MET cc_start: 0.9028 (tmm) cc_final: 0.8765 (tmm) REVERT: C 383 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 429 ASN cc_start: 0.8503 (m-40) cc_final: 0.8142 (m-40) REVERT: C 587 ASP cc_start: 0.8382 (t0) cc_final: 0.8155 (t70) REVERT: C 710 MET cc_start: 0.8382 (ppp) cc_final: 0.8079 (ppp) REVERT: C 951 VAL cc_start: 0.8859 (t) cc_final: 0.8624 (p) REVERT: C 1064 TYR cc_start: 0.7375 (m-10) cc_final: 0.7132 (m-10) REVERT: D 19 ASP cc_start: 0.8421 (t0) cc_final: 0.8183 (t0) REVERT: D 30 LYS cc_start: 0.9045 (tptm) cc_final: 0.8796 (tptm) REVERT: D 103 HIS cc_start: 0.6322 (t70) cc_final: 0.6093 (t70) REVERT: D 264 ARG cc_start: 0.8591 (tpm170) cc_final: 0.8199 (tpm170) REVERT: D 296 LEU cc_start: 0.9220 (mt) cc_final: 0.9005 (mt) REVERT: D 356 ARG cc_start: 0.8400 (tpm170) cc_final: 0.8129 (tpm170) REVERT: D 373 MET cc_start: 0.7600 (tpp) cc_final: 0.7294 (tpp) REVERT: D 405 MET cc_start: 0.8004 (tpp) cc_final: 0.7703 (tpp) REVERT: D 590 THR cc_start: 0.6231 (m) cc_final: 0.6015 (m) REVERT: D 919 MET cc_start: 0.7677 (mmm) cc_final: 0.7132 (mmm) REVERT: D 971 MET cc_start: 0.8238 (ppp) cc_final: 0.7950 (ppp) REVERT: E 79 LEU cc_start: 0.8391 (mp) cc_final: 0.7816 (tt) REVERT: F 229 ASN cc_start: 0.8841 (t0) cc_final: 0.8449 (p0) REVERT: F 231 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8585 (pp20) REVERT: F 298 MET cc_start: 0.6847 (ttp) cc_final: 0.6448 (ttt) REVERT: F 342 MET cc_start: 0.7724 (ppp) cc_final: 0.7282 (ppp) REVERT: F 355 MET cc_start: 0.8717 (tpp) cc_final: 0.8394 (tpp) REVERT: F 398 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8686 (mmtt) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.1928 time to fit residues: 141.2847 Evaluate side-chains 344 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 354 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 89 HIS B 151 GLN C 372 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093916 restraints weight = 111452.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094124 restraints weight = 77371.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094594 restraints weight = 61865.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095402 restraints weight = 51452.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095382 restraints weight = 45471.002| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31481 Z= 0.167 Angle : 0.637 11.698 43317 Z= 0.335 Chirality : 0.042 0.335 4923 Planarity : 0.004 0.054 5067 Dihedral : 20.685 179.473 5662 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.03 % Allowed : 1.03 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3458 helix: 0.94 (0.14), residues: 1403 sheet: -0.59 (0.24), residues: 415 loop : -0.54 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 203 TYR 0.021 0.002 TYR E 32 PHE 0.019 0.002 PHE F 436 TRP 0.016 0.002 TRP C 924 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00380 (31453) covalent geometry : angle 0.62548 (43293) hydrogen bonds : bond 0.04001 ( 1408) hydrogen bonds : angle 4.36581 ( 3864) metal coordination : bond 0.00642 ( 28) metal coordination : angle 5.13901 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8177 (ttm) cc_final: 0.7689 (tpp) REVERT: A 177 LYS cc_start: 0.8811 (ptmm) cc_final: 0.8529 (ptmm) REVERT: A 202 MET cc_start: 0.8526 (pmm) cc_final: 0.8139 (pmm) REVERT: B 5 GLN cc_start: 0.8008 (mp10) cc_final: 0.7789 (mp10) REVERT: B 82 GLN cc_start: 0.8449 (tt0) cc_final: 0.7854 (pt0) REVERT: C 148 MET cc_start: 0.8581 (tpt) cc_final: 0.8189 (tpt) REVERT: C 382 MET cc_start: 0.8986 (tmm) cc_final: 0.8713 (tmm) REVERT: C 383 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7770 (mt-10) REVERT: C 593 MET cc_start: 0.8055 (mmm) cc_final: 0.7758 (mmm) REVERT: C 710 MET cc_start: 0.8419 (ppp) cc_final: 0.8153 (ppp) REVERT: C 725 GLN cc_start: 0.7309 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 980 ASN cc_start: 0.7694 (p0) cc_final: 0.7097 (m-40) REVERT: C 992 LYS cc_start: 0.7400 (mttm) cc_final: 0.6936 (mtpt) REVERT: C 1064 TYR cc_start: 0.7491 (m-10) cc_final: 0.7264 (m-10) REVERT: D 19 ASP cc_start: 0.8475 (t0) cc_final: 0.8215 (t70) REVERT: D 30 LYS cc_start: 0.9030 (tptm) cc_final: 0.8777 (tptm) REVERT: D 103 HIS cc_start: 0.6395 (t-90) cc_final: 0.5622 (t-170) REVERT: D 232 GLN cc_start: 0.8551 (mt0) cc_final: 0.8247 (mp10) REVERT: D 296 LEU cc_start: 0.9203 (mt) cc_final: 0.8924 (mt) REVERT: D 356 ARG cc_start: 0.8426 (tpm170) cc_final: 0.8147 (tpm170) REVERT: D 405 MET cc_start: 0.8071 (tpp) cc_final: 0.7786 (tpp) REVERT: D 491 ILE cc_start: 0.7819 (pt) cc_final: 0.7596 (pt) REVERT: D 590 THR cc_start: 0.6325 (m) cc_final: 0.6035 (m) REVERT: D 612 MET cc_start: 0.8981 (mtp) cc_final: 0.8763 (tpp) REVERT: D 808 GLN cc_start: 0.8731 (mp10) cc_final: 0.8383 (mp10) REVERT: D 919 MET cc_start: 0.7725 (mmm) cc_final: 0.7158 (mmm) REVERT: D 971 MET cc_start: 0.8309 (ppp) cc_final: 0.7944 (ppp) REVERT: E 79 LEU cc_start: 0.8424 (mp) cc_final: 0.7890 (tt) REVERT: F 229 ASN cc_start: 0.8774 (t0) cc_final: 0.8442 (p0) REVERT: F 231 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8727 (tm-30) REVERT: F 342 MET cc_start: 0.7826 (ppp) cc_final: 0.7302 (ppp) REVERT: F 355 MET cc_start: 0.8757 (tpp) cc_final: 0.8462 (tpp) REVERT: F 432 ASP cc_start: 0.8992 (m-30) cc_final: 0.8779 (m-30) outliers start: 1 outliers final: 0 residues processed: 432 average time/residue: 0.1901 time to fit residues: 131.0042 Evaluate side-chains 336 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 204 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 316 optimal weight: 0.8980 chunk 348 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 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 = 0.4271 r_free = 0.4271 target = 0.132980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094817 restraints weight = 111713.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094708 restraints weight = 82967.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.096308 restraints weight = 60019.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096413 restraints weight = 49014.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096475 restraints weight = 43787.148| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31481 Z= 0.141 Angle : 0.631 15.155 43317 Z= 0.328 Chirality : 0.042 0.342 4923 Planarity : 0.004 0.052 5067 Dihedral : 20.651 179.981 5662 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3458 helix: 0.95 (0.14), residues: 1402 sheet: -0.63 (0.24), residues: 410 loop : -0.52 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 203 TYR 0.021 0.001 TYR E 32 PHE 0.020 0.002 PHE A 17 TRP 0.019 0.001 TRP C 924 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00320 (31453) covalent geometry : angle 0.61503 (43293) hydrogen bonds : bond 0.03863 ( 1408) hydrogen bonds : angle 4.33696 ( 3864) metal coordination : bond 0.00522 ( 28) metal coordination : angle 5.97441 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8843 (ptmm) cc_final: 0.8551 (ptmm) REVERT: A 202 MET cc_start: 0.8617 (pmm) cc_final: 0.8229 (pmm) REVERT: B 2 LEU cc_start: 0.9145 (pp) cc_final: 0.8901 (tp) REVERT: B 82 GLN cc_start: 0.8506 (tt0) cc_final: 0.7871 (pt0) REVERT: C 148 MET cc_start: 0.8550 (tpt) cc_final: 0.8159 (tpt) REVERT: C 209 MET cc_start: 0.7226 (mmp) cc_final: 0.5990 (mmp) REVERT: C 356 ILE cc_start: 0.9220 (pt) cc_final: 0.8896 (pt) REVERT: C 362 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7468 (mtt-85) REVERT: C 382 MET cc_start: 0.8980 (tmm) cc_final: 0.8750 (tmm) REVERT: C 593 MET cc_start: 0.7996 (mmm) cc_final: 0.7725 (mmm) REVERT: C 710 MET cc_start: 0.8348 (ppp) cc_final: 0.8097 (ppp) REVERT: C 744 ASP cc_start: 0.6812 (p0) cc_final: 0.6571 (p0) REVERT: D 19 ASP cc_start: 0.8467 (t0) cc_final: 0.8201 (t70) REVERT: D 30 LYS cc_start: 0.9007 (tptm) cc_final: 0.8755 (tptm) REVERT: D 232 GLN cc_start: 0.8551 (mt0) cc_final: 0.8304 (mp10) REVERT: D 296 LEU cc_start: 0.9193 (mt) cc_final: 0.8880 (mt) REVERT: D 352 ASN cc_start: 0.8536 (m-40) cc_final: 0.8314 (m110) REVERT: D 356 ARG cc_start: 0.8406 (tpm170) cc_final: 0.8115 (tpm170) REVERT: D 399 LEU cc_start: 0.7904 (mt) cc_final: 0.7625 (mt) REVERT: D 405 MET cc_start: 0.7993 (tpp) cc_final: 0.7714 (tpp) REVERT: D 428 SER cc_start: 0.9305 (m) cc_final: 0.9065 (m) REVERT: D 612 MET cc_start: 0.8922 (mtp) cc_final: 0.8703 (tpp) REVERT: D 626 ASP cc_start: 0.8184 (t0) cc_final: 0.7954 (t0) REVERT: D 808 GLN cc_start: 0.8765 (mp10) cc_final: 0.8368 (mp10) REVERT: D 919 MET cc_start: 0.7688 (mmm) cc_final: 0.7186 (mmm) REVERT: D 971 MET cc_start: 0.8049 (ppp) cc_final: 0.7742 (ppp) REVERT: D 1224 LYS cc_start: 0.7896 (pptt) cc_final: 0.7591 (mmmt) REVERT: F 229 ASN cc_start: 0.8753 (t0) cc_final: 0.8446 (p0) REVERT: F 299 LEU cc_start: 0.8707 (mm) cc_final: 0.8503 (mm) REVERT: F 342 MET cc_start: 0.7818 (ppp) cc_final: 0.7258 (ppp) REVERT: F 355 MET cc_start: 0.8775 (tpp) cc_final: 0.8484 (tpp) REVERT: F 398 LYS cc_start: 0.8966 (mmtp) cc_final: 0.8712 (mmtt) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2038 time to fit residues: 140.9783 Evaluate side-chains 339 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 12 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 255 optimal weight: 0.0030 chunk 14 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 327 optimal weight: 40.0000 chunk 254 optimal weight: 0.8980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** D 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 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 = 0.4264 r_free = 0.4264 target = 0.132472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093734 restraints weight = 110437.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094783 restraints weight = 80620.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095549 restraints weight = 56344.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095980 restraints weight = 47426.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096232 restraints weight = 42488.326| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31481 Z= 0.144 Angle : 0.639 15.407 43317 Z= 0.331 Chirality : 0.042 0.308 4923 Planarity : 0.005 0.142 5067 Dihedral : 20.644 179.821 5662 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3458 helix: 0.91 (0.14), residues: 1408 sheet: -0.61 (0.24), residues: 409 loop : -0.54 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 113 TYR 0.022 0.001 TYR E 32 PHE 0.019 0.002 PHE A 17 TRP 0.024 0.001 TRP D 105 HIS 0.008 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00327 (31453) covalent geometry : angle 0.62577 (43293) hydrogen bonds : bond 0.03826 ( 1408) hydrogen bonds : angle 4.30917 ( 3864) metal coordination : bond 0.00537 ( 28) metal coordination : angle 5.59775 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.9065 (tp) cc_final: 0.8790 (tp) REVERT: A 177 LYS cc_start: 0.8825 (ptmm) cc_final: 0.8544 (ptmm) REVERT: A 202 MET cc_start: 0.8559 (pmm) cc_final: 0.8134 (pmm) REVERT: B 2 LEU cc_start: 0.9169 (pp) cc_final: 0.8924 (tp) REVERT: B 5 GLN cc_start: 0.8003 (mp10) cc_final: 0.7758 (mp10) REVERT: B 82 GLN cc_start: 0.8495 (tt0) cc_final: 0.7900 (pt0) REVERT: C 148 MET cc_start: 0.8534 (tpt) cc_final: 0.8198 (tpt) REVERT: C 209 MET cc_start: 0.7338 (mmp) cc_final: 0.6233 (mmm) REVERT: C 356 ILE cc_start: 0.9179 (pt) cc_final: 0.8868 (pt) REVERT: C 362 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7461 (mtt-85) REVERT: C 382 MET cc_start: 0.8972 (tmm) cc_final: 0.8755 (tmm) REVERT: C 593 MET cc_start: 0.7966 (mmm) cc_final: 0.7746 (mmm) REVERT: C 710 MET cc_start: 0.8335 (ppp) cc_final: 0.8101 (ppp) REVERT: C 725 GLN cc_start: 0.7305 (tm-30) cc_final: 0.7068 (tm-30) REVERT: C 922 LEU cc_start: 0.9102 (tp) cc_final: 0.8841 (tp) REVERT: C 992 LYS cc_start: 0.7033 (mmmt) cc_final: 0.6614 (mtpt) REVERT: D 19 ASP cc_start: 0.8446 (t0) cc_final: 0.8244 (t70) REVERT: D 232 GLN cc_start: 0.8590 (mt0) cc_final: 0.8336 (mp10) REVERT: D 296 LEU cc_start: 0.9135 (mt) cc_final: 0.8799 (mt) REVERT: D 356 ARG cc_start: 0.8401 (tpm170) cc_final: 0.8113 (tpm170) REVERT: D 405 MET cc_start: 0.7971 (tpp) cc_final: 0.7681 (tpp) REVERT: D 590 THR cc_start: 0.6499 (m) cc_final: 0.6280 (m) REVERT: D 612 MET cc_start: 0.8885 (mtp) cc_final: 0.8640 (tpp) REVERT: D 626 ASP cc_start: 0.8060 (t0) cc_final: 0.7839 (t0) REVERT: D 808 GLN cc_start: 0.8701 (mp10) cc_final: 0.8349 (mp10) REVERT: D 809 MET cc_start: 0.8710 (ptm) cc_final: 0.8483 (ppp) REVERT: D 872 LEU cc_start: 0.9040 (mt) cc_final: 0.8690 (mt) REVERT: D 919 MET cc_start: 0.7714 (mmm) cc_final: 0.7231 (mmm) REVERT: D 971 MET cc_start: 0.7960 (ppp) cc_final: 0.7618 (ppp) REVERT: F 229 ASN cc_start: 0.8766 (t0) cc_final: 0.8337 (p0) REVERT: F 231 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8582 (pp20) REVERT: F 342 MET cc_start: 0.7816 (ppp) cc_final: 0.7257 (ppp) REVERT: F 355 MET cc_start: 0.8679 (tpp) cc_final: 0.8416 (tpp) REVERT: F 398 LYS cc_start: 0.9006 (mmtp) cc_final: 0.8774 (mmtt) REVERT: F 406 LEU cc_start: 0.4962 (mp) cc_final: 0.4658 (mp) REVERT: F 432 ASP cc_start: 0.9054 (m-30) cc_final: 0.8642 (m-30) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.2003 time to fit residues: 137.5285 Evaluate side-chains 334 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 305 optimal weight: 0.0270 chunk 300 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 342 optimal weight: 50.0000 chunk 287 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 151 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 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 = 0.4277 r_free = 0.4277 target = 0.133343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095736 restraints weight = 110686.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096100 restraints weight = 77571.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097033 restraints weight = 56972.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097219 restraints weight = 51856.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097531 restraints weight = 43889.545| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31481 Z= 0.129 Angle : 0.631 13.427 43317 Z= 0.327 Chirality : 0.042 0.305 4923 Planarity : 0.004 0.077 5067 Dihedral : 20.610 179.547 5662 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3458 helix: 0.93 (0.14), residues: 1403 sheet: -0.50 (0.25), residues: 406 loop : -0.54 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.021 0.001 TYR E 32 PHE 0.017 0.001 PHE B 63 TRP 0.014 0.001 TRP D 105 HIS 0.009 0.001 HIS D 849 Details of bonding type rmsd covalent geometry : bond 0.00290 (31453) covalent geometry : angle 0.61769 (43293) hydrogen bonds : bond 0.03734 ( 1408) hydrogen bonds : angle 4.26218 ( 3864) metal coordination : bond 0.00402 ( 28) metal coordination : angle 5.41146 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5648.73 seconds wall clock time: 98 minutes 28.42 seconds (5908.42 seconds total)