Starting phenix.real_space_refine on Mon Sep 14 13:44:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vpz_32077/09_2026/7vpz_32077_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vpz_32077/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vpz_32077/09_2026/7vpz_32077_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vpz_32077/09_2026/7vpz_32077_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vpz_32077/09_2026/7vpz_32077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vpz_32077/09_2026/7vpz_32077.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.48, per 1000 atoms: 0.18 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 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: 4.06 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: 7.33 Time building geometry restraints manager: 3.13 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=" C1' DC O 8 " pdb=" N1 DC O 8 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.01e+01 bond pdb=" C1' DC P 16 " pdb=" N1 DC P 16 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" C1' DC P 24 " pdb=" N1 DC P 24 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" C1' DG P 15 " pdb=" N9 DG P 15 " ideal model delta sigma weight residual 1.468 1.402 0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" C1' DC P 67 " pdb=" N1 DC P 67 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.08e+01 ... (remaining 31448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 42569 2.75 - 5.50: 678 5.50 - 8.25: 37 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: 4503 0.098 - 0.196: 398 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: 3.730 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 32.890 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.077 31481 Z= 0.358 Angle : 0.829 13.742 43317 Z= 0.536 Chirality : 0.054 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/Z covalent geometry : bond 0.00513 / 0.36 (31453) covalent geometry : angle 0.81711 / 0.54 (43293) hydrogen bonds : bond 0.14747 / 10.62 ( 1408) hydrogen bonds : angle 5.98346 / 4.20 ( 3864) metal coordination : bond 0.00556 / 0.31 ( 28) metal coordination : angle 5.95049 / 3.25 ( 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 : 1.073 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: 0.6900 (mp10) REVERT: B 150 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7704 (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: 0.8650 (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: 0.8471 (mmtt) REVERT: C 725 GLN cc_start: 0.6764 (tm-30) cc_final: 0.6382 (tm-30) REVERT: D 19 ASP cc_start: 0.8431 (t0) cc_final: 0.8174 (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: 0.8067 (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: 0.4876 (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: 0.8667 (tp40) REVERT: D 1191 MET cc_start: 0.7748 (pmm) cc_final: 0.7523 (pmm) REVERT: E 18 GLU cc_start: 0.8576 (mp0) cc_final: 0.8357 (pm20) REVERT: E 26 LYS cc_start: 0.8481 (mttt) cc_final: 0.7840 (mmmm) REVERT: E 70 ILE cc_start: 0.8844 (mp) cc_final: 0.8570 (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: 0.2101 time to fit residues: 180.5956 Evaluate side-chains 396 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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... A 36 ASN B 151 GLN B 185 GLN C 220 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN C 921 HIS D 103 HIS ** 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 ** 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 = 0.4310 r_free = 0.4310 target = 0.136320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097551 restraints weight = 108715.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098837 restraints weight = 71824.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099308 restraints weight = 54027.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.099810 restraints weight = 45738.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.100170 restraints weight = 38625.039| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31481 Z= 0.166 Angle : 0.702 12.289 43317 Z= 0.378 Chirality : 0.048 0.388 4923 Planarity : 0.005 0.068 5067 Dihedral : 20.994 179.404 5662 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.14 % Allowed : 4.64 % Favored : 95.22 % 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: 0.92 (0.13), residues: 1403 sheet: -0.80 (0.25), residues: 400 loop : -0.56 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 245 TYR 0.022 0.002 TYR E 32 PHE 0.033 0.002 PHE D1209 TRP 0.020 0.002 TRP D1203 HIS 0.005 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (31453) covalent geometry : angle 0.69196 / 0.38 (43293) hydrogen bonds : bond 0.05415 / 3.85 ( 1408) hydrogen bonds : angle 4.89091 / 3.45 ( 3864) metal coordination : bond 0.00551 / 0.29 ( 28) metal coordination : angle 5.12076 / 3.00 ( 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 508 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 504 time to evaluate : 1.167 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: A 81 LYS cc_start: 0.9153 (pptt) cc_final: 0.8851 (ptpt) REVERT: B 5 GLN cc_start: 0.7277 (mp10) cc_final: 0.6907 (mp10) REVERT: B 152 ASN cc_start: 0.7450 (m-40) cc_final: 0.7230 (m-40) REVERT: C 76 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8793 (tm-30) REVERT: C 201 GLU cc_start: 0.6796 (mp0) cc_final: 0.6581 (mp0) REVERT: C 269 LEU cc_start: 0.9174 (mm) cc_final: 0.8757 (tp) REVERT: C 382 MET cc_start: 0.9039 (tmm) cc_final: 0.8551 (tmm) REVERT: C 383 GLU cc_start: 0.8463 (tt0) cc_final: 0.8222 (mt-10) REVERT: C 438 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8388 (mmtt) REVERT: C 473 GLU cc_start: 0.7885 (pt0) cc_final: 0.7551 (pt0) REVERT: C 701 LEU cc_start: 0.8355 (mp) cc_final: 0.8098 (mm) REVERT: C 725 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6469 (tm-30) REVERT: C 839 PHE cc_start: 0.7163 (m-10) cc_final: 0.6871 (m-10) REVERT: C 1053 PHE cc_start: 0.6427 (t80) cc_final: 0.6171 (t80) REVERT: C 1119 ASN cc_start: 0.6598 (p0) cc_final: 0.6372 (t0) REVERT: D 19 ASP cc_start: 0.8308 (t0) cc_final: 0.8079 (t0) REVERT: D 154 HIS cc_start: 0.9327 (m90) cc_final: 0.8991 (m90) REVERT: D 160 GLN cc_start: 0.9516 (OUTLIER) cc_final: 0.9256 (pp30) REVERT: D 252 PHE cc_start: 0.8399 (p90) cc_final: 0.7916 (p90) REVERT: D 264 ARG cc_start: 0.8465 (tpm170) cc_final: 0.8253 (tpm170) REVERT: D 296 LEU cc_start: 0.9232 (mt) cc_final: 0.8823 (mt) REVERT: D 356 ARG cc_start: 0.8253 (tpm170) cc_final: 0.7953 (tpm170) REVERT: D 373 MET cc_start: 0.7635 (tpp) cc_final: 0.6794 (tpp) REVERT: D 470 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9170 (mmtm) REVERT: D 475 MET cc_start: 0.8939 (tpt) cc_final: 0.8681 (tpt) REVERT: D 831 ILE cc_start: 0.9277 (mt) cc_final: 0.8860 (mt) REVERT: D 843 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 881 ILE cc_start: 0.7691 (mm) cc_final: 0.7485 (mm) REVERT: D 919 MET cc_start: 0.7150 (mmm) cc_final: 0.6514 (mmm) REVERT: E 60 ASP cc_start: 0.8261 (p0) cc_final: 0.7957 (p0) REVERT: E 70 ILE cc_start: 0.8664 (mp) cc_final: 0.8424 (mp) REVERT: F 229 ASN cc_start: 0.8842 (t0) cc_final: 0.8351 (p0) REVERT: F 342 MET cc_start: 0.7638 (ppp) cc_final: 0.7172 (ppp) REVERT: F 360 ASN cc_start: 0.9391 (p0) cc_final: 0.9189 (p0) outliers start: 4 outliers final: 0 residues processed: 507 average time/residue: 0.2200 time to fit residues: 173.7844 Evaluate side-chains 370 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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: 2.9990 chunk 134 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 248 optimal weight: 0.0370 chunk 182 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 330 optimal weight: 50.0000 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.136437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097422 restraints weight = 108547.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099304 restraints weight = 71119.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099946 restraints weight = 47754.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.100442 restraints weight = 41424.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100496 restraints weight = 37398.920| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31481 Z= 0.149 Angle : 0.665 11.477 43317 Z= 0.356 Chirality : 0.047 0.355 4923 Planarity : 0.005 0.090 5067 Dihedral : 20.991 179.975 5662 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.36 % 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: 0.86 (0.13), residues: 1404 sheet: -0.75 (0.24), residues: 403 loop : -0.51 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 386 TYR 0.035 0.002 TYR E 32 PHE 0.021 0.002 PHE D 268 TRP 0.028 0.002 TRP C 924 HIS 0.008 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (31453) covalent geometry : angle 0.65420 / 0.36 (43293) hydrogen bonds : bond 0.04865 / 3.46 ( 1408) hydrogen bonds : angle 4.69740 / 3.30 ( 3864) metal coordination : bond 0.00382 / 0.19 ( 28) metal coordination : angle 5.01115 / 2.95 ( 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 495 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 1.132 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: A 81 LYS cc_start: 0.9063 (pptt) cc_final: 0.8819 (ptpt) REVERT: B 5 GLN cc_start: 0.7419 (mp10) cc_final: 0.6901 (mp10) REVERT: B 152 ASN cc_start: 0.7491 (m-40) cc_final: 0.7226 (m-40) REVERT: C 76 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8725 (tm-30) REVERT: C 193 ILE cc_start: 0.8447 (tp) cc_final: 0.8158 (tp) REVERT: C 269 LEU cc_start: 0.9184 (mm) cc_final: 0.8776 (tp) REVERT: C 382 MET cc_start: 0.9050 (tmm) cc_final: 0.8625 (tmm) REVERT: C 383 GLU cc_start: 0.8534 (tt0) cc_final: 0.8229 (mt-10) REVERT: C 438 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8332 (mmtt) REVERT: C 473 GLU cc_start: 0.7806 (pt0) cc_final: 0.7578 (pt0) REVERT: C 593 MET cc_start: 0.7737 (mmm) cc_final: 0.7453 (mmm) REVERT: C 701 LEU cc_start: 0.7863 (mp) cc_final: 0.7312 (mp) REVERT: C 725 GLN cc_start: 0.6883 (tm-30) cc_final: 0.6549 (tm-30) REVERT: C 1053 PHE cc_start: 0.6563 (t80) cc_final: 0.6157 (t80) REVERT: C 1119 ASN cc_start: 0.6620 (p0) cc_final: 0.6376 (t0) REVERT: D 19 ASP cc_start: 0.8341 (t0) cc_final: 0.8052 (t0) REVERT: D 29 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8505 (mtmt) REVERT: D 103 HIS cc_start: 0.6278 (t70) cc_final: 0.5781 (t70) REVERT: D 154 HIS cc_start: 0.9362 (m90) cc_final: 0.9053 (m90) REVERT: D 264 ARG cc_start: 0.8553 (tpm170) cc_final: 0.8281 (tpm170) REVERT: D 296 LEU cc_start: 0.9271 (mt) cc_final: 0.8795 (mt) REVERT: D 314 LEU cc_start: 0.8362 (pt) cc_final: 0.8152 (pt) REVERT: D 356 ARG cc_start: 0.8311 (tpm170) cc_final: 0.8084 (tpm170) REVERT: D 373 MET cc_start: 0.7614 (tpp) cc_final: 0.6770 (tpp) REVERT: D 457 MET cc_start: 0.7184 (ttt) cc_final: 0.6979 (tpp) REVERT: D 470 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9031 (mmtm) REVERT: D 807 MET cc_start: 0.8845 (pmm) cc_final: 0.8548 (pmm) REVERT: D 831 ILE cc_start: 0.9256 (mt) cc_final: 0.8878 (mt) REVERT: D 843 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8109 (mt-10) REVERT: D 919 MET cc_start: 0.7015 (mmm) cc_final: 0.6785 (mmp) REVERT: F 229 ASN cc_start: 0.8774 (t0) cc_final: 0.8344 (p0) REVERT: F 298 MET cc_start: 0.6735 (ttp) cc_final: 0.6344 (ttt) REVERT: F 342 MET cc_start: 0.7767 (ppp) cc_final: 0.7233 (ppp) outliers start: 2 outliers final: 0 residues processed: 495 average time/residue: 0.2129 time to fit residues: 166.4302 Evaluate side-chains 368 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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: 50.0000 chunk 144 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 151 GLN C 465 HIS ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** 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 494 HIS D 544 HIS ** 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 252 ASN F 336 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.134379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.096747 restraints weight = 110063.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096845 restraints weight = 69959.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097630 restraints weight = 53713.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098003 restraints weight = 47567.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098258 restraints weight = 42743.483| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31481 Z= 0.175 Angle : 0.667 14.001 43317 Z= 0.358 Chirality : 0.046 0.353 4923 Planarity : 0.005 0.062 5067 Dihedral : 20.917 179.239 5662 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.03 % Allowed : 3.47 % 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: -0.06 (0.14), residues: 3458 helix: 0.85 (0.13), residues: 1394 sheet: -0.72 (0.24), residues: 414 loop : -0.56 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 890 TYR 0.029 0.002 TYR E 32 PHE 0.031 0.002 PHE D1209 TRP 0.024 0.002 TRP C 924 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (31453) covalent geometry : angle 0.65608 / 0.36 (43293) hydrogen bonds : bond 0.04629 / 3.27 ( 1408) hydrogen bonds : angle 4.62503 / 3.26 ( 3864) metal coordination : bond 0.00672 / 0.33 ( 28) metal coordination : angle 5.16879 / 2.99 ( 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 468 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 1.110 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: A 81 LYS cc_start: 0.9102 (pptt) cc_final: 0.8721 (ptpp) REVERT: B 5 GLN cc_start: 0.7350 (mp10) cc_final: 0.7026 (mp10) REVERT: B 152 ASN cc_start: 0.7588 (m-40) cc_final: 0.7270 (m-40) REVERT: C 76 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8872 (tm-30) REVERT: C 181 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9480 (mmtm) REVERT: C 269 LEU cc_start: 0.9190 (mm) cc_final: 0.8809 (tp) REVERT: C 382 MET cc_start: 0.9094 (tmm) cc_final: 0.8777 (tmm) REVERT: C 438 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8368 (mttt) REVERT: C 587 ASP cc_start: 0.8480 (t70) cc_final: 0.8214 (t70) REVERT: C 593 MET cc_start: 0.7743 (mmm) cc_final: 0.7373 (mmm) REVERT: C 725 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6630 (tm-30) REVERT: C 911 ARG cc_start: 0.7861 (mpt-90) cc_final: 0.6531 (mmp80) REVERT: C 980 ASN cc_start: 0.7353 (p0) cc_final: 0.7124 (m-40) REVERT: C 1053 PHE cc_start: 0.6927 (t80) cc_final: 0.6420 (t80) REVERT: C 1119 ASN cc_start: 0.6746 (p0) cc_final: 0.6457 (t0) REVERT: D 19 ASP cc_start: 0.8503 (t0) cc_final: 0.8120 (t70) REVERT: D 29 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8483 (mtmm) REVERT: D 103 HIS cc_start: 0.6589 (t70) cc_final: 0.6312 (t70) REVERT: D 154 HIS cc_start: 0.9407 (m90) cc_final: 0.9049 (m90) REVERT: D 264 ARG cc_start: 0.8651 (tpm170) cc_final: 0.8307 (tpm170) REVERT: D 296 LEU cc_start: 0.9266 (mt) cc_final: 0.8819 (mt) REVERT: D 314 LEU cc_start: 0.8303 (pt) cc_final: 0.8092 (pt) REVERT: D 356 ARG cc_start: 0.8437 (tpm170) cc_final: 0.8180 (tpm170) REVERT: D 373 MET cc_start: 0.7485 (tpp) cc_final: 0.6875 (tpp) REVERT: D 449 LEU cc_start: 0.8911 (mt) cc_final: 0.8697 (mt) REVERT: D 457 MET cc_start: 0.7304 (ttt) cc_final: 0.6947 (tpp) REVERT: D 470 LYS cc_start: 0.9454 (mmmm) cc_final: 0.9076 (mmtm) REVERT: D 721 ARG cc_start: 0.7124 (tpp80) cc_final: 0.6666 (tpp80) REVERT: D 745 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8252 (mm-30) REVERT: D 831 ILE cc_start: 0.9311 (mt) cc_final: 0.9079 (mt) REVERT: D 843 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8018 (mt-10) REVERT: E 79 LEU cc_start: 0.8599 (mp) cc_final: 0.8255 (tt) REVERT: F 229 ASN cc_start: 0.8807 (t0) cc_final: 0.8310 (p0) REVERT: F 324 TYR cc_start: 0.8096 (m-80) cc_final: 0.7694 (m-80) REVERT: F 342 MET cc_start: 0.7748 (ppp) cc_final: 0.7233 (ppp) REVERT: F 420 ASP cc_start: 0.8515 (m-30) cc_final: 0.8261 (m-30) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.2111 time to fit residues: 156.3915 Evaluate side-chains 361 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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: 10.0000 chunk 189 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 241 optimal weight: 3.9990 chunk 307 optimal weight: 0.0070 chunk 203 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 200 GLN B 151 GLN ** C 529 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 778 ASN 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 = 0.4291 r_free = 0.4291 target = 0.134910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096114 restraints weight = 109296.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096392 restraints weight = 75009.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097697 restraints weight = 58785.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098240 restraints weight = 43773.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.098367 restraints weight = 40693.414| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31481 Z= 0.148 Angle : 0.640 15.004 43317 Z= 0.341 Chirality : 0.046 0.350 4923 Planarity : 0.004 0.052 5067 Dihedral : 20.885 178.921 5662 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.22 % 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: 0.01 (0.14), residues: 3458 helix: 0.88 (0.14), residues: 1404 sheet: -0.56 (0.24), residues: 410 loop : -0.53 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 453 TYR 0.030 0.002 TYR E 32 PHE 0.031 0.002 PHE D1209 TRP 0.028 0.002 TRP C 924 HIS 0.006 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (31453) covalent geometry : angle 0.62771 / 0.34 (43293) hydrogen bonds : bond 0.04375 / 3.08 ( 1408) hydrogen bonds : angle 4.50782 / 3.17 ( 3864) metal coordination : bond 0.00508 / 0.24 ( 28) metal coordination : angle 5.37755 / 3.02 ( 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 484 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 1.159 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: A 81 LYS cc_start: 0.9127 (pptt) cc_final: 0.8710 (ptpp) REVERT: B 5 GLN cc_start: 0.7383 (mp10) cc_final: 0.7152 (mp10) REVERT: B 152 ASN cc_start: 0.7460 (m-40) cc_final: 0.7074 (m-40) REVERT: B 202 MET cc_start: 0.7832 (mtt) cc_final: 0.7597 (mtm) REVERT: C 76 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8731 (tm-30) REVERT: C 111 LYS cc_start: 0.8714 (ptpp) cc_final: 0.8492 (pttt) REVERT: C 148 MET cc_start: 0.8502 (tpt) cc_final: 0.8256 (tpt) REVERT: C 181 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9473 (mmtm) REVERT: C 201 GLU cc_start: 0.6586 (mp0) cc_final: 0.6296 (mp0) REVERT: C 269 LEU cc_start: 0.9186 (mm) cc_final: 0.8811 (tp) REVERT: C 356 ILE cc_start: 0.9175 (pt) cc_final: 0.8828 (pt) REVERT: C 382 MET cc_start: 0.9041 (tmm) cc_final: 0.8673 (tmm) REVERT: C 383 GLU cc_start: 0.8318 (tt0) cc_final: 0.7931 (mt-10) REVERT: C 438 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8337 (mttt) REVERT: C 587 ASP cc_start: 0.8483 (t70) cc_final: 0.8239 (t70) REVERT: C 1053 PHE cc_start: 0.7056 (t80) cc_final: 0.6555 (t80) REVERT: C 1119 ASN cc_start: 0.6773 (p0) cc_final: 0.6413 (t0) REVERT: D 19 ASP cc_start: 0.8412 (t0) cc_final: 0.8068 (t70) REVERT: D 29 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8614 (mtmm) REVERT: D 154 HIS cc_start: 0.9418 (m90) cc_final: 0.9054 (m90) REVERT: D 264 ARG cc_start: 0.8661 (tpm170) cc_final: 0.8267 (tpm170) REVERT: D 296 LEU cc_start: 0.9146 (mt) cc_final: 0.8685 (mt) REVERT: D 314 LEU cc_start: 0.8268 (pt) cc_final: 0.8047 (pt) REVERT: D 356 ARG cc_start: 0.8388 (tpm170) cc_final: 0.8087 (tpm170) REVERT: D 373 MET cc_start: 0.7578 (tpp) cc_final: 0.7071 (tpp) REVERT: D 457 MET cc_start: 0.7259 (ttt) cc_final: 0.6886 (tpp) REVERT: D 470 LYS cc_start: 0.9411 (mmmm) cc_final: 0.9068 (mmtm) REVERT: D 590 THR cc_start: 0.6709 (m) cc_final: 0.6478 (m) REVERT: D 721 ARG cc_start: 0.7048 (tpp80) cc_final: 0.6418 (tpp80) REVERT: D 808 GLN cc_start: 0.8850 (mp10) cc_final: 0.8342 (mp10) REVERT: D 831 ILE cc_start: 0.9267 (mt) cc_final: 0.9028 (mt) REVERT: D 843 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 919 MET cc_start: 0.7042 (mmm) cc_final: 0.6771 (mmm) REVERT: E 75 ILE cc_start: 0.8223 (mm) cc_final: 0.8016 (mm) REVERT: F 229 ASN cc_start: 0.8700 (t0) cc_final: 0.8253 (p0) REVERT: F 324 TYR cc_start: 0.8005 (m-80) cc_final: 0.7679 (m-80) REVERT: F 342 MET cc_start: 0.7739 (ppp) cc_final: 0.7202 (ppp) outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.2113 time to fit residues: 162.0997 Evaluate side-chains 359 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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: 0.0670 chunk 232 optimal weight: 0.8980 chunk 330 optimal weight: 50.0000 chunk 116 optimal weight: 3.9990 chunk 337 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 83 optimal weight: 0.0040 chunk 326 optimal weight: 7.9990 overall best weight: 1.7934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 151 GLN ** C 529 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1182 HIS F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.132960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094708 restraints weight = 110613.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094575 restraints weight = 73332.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095080 restraints weight = 55864.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095536 restraints weight = 50936.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096082 restraints weight = 44331.297| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2688 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= 0.192 Angle : 0.677 14.126 43317 Z= 0.361 Chirality : 0.047 0.347 4923 Planarity : 0.005 0.096 5067 Dihedral : 20.882 177.773 5662 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % 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: -0.12 (0.14), residues: 3458 helix: 0.80 (0.13), residues: 1397 sheet: -0.73 (0.24), residues: 426 loop : -0.59 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 453 TYR 0.024 0.002 TYR E 32 PHE 0.035 0.002 PHE A 189 TRP 0.030 0.002 TRP C 924 HIS 0.005 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (31453) covalent geometry : angle 0.66579 / 0.36 (43293) hydrogen bonds : bond 0.04486 / 3.13 ( 1408) hydrogen bonds : angle 4.61597 / 3.24 ( 3864) metal coordination : bond 0.01086 / 0.65 ( 28) metal coordination : angle 5.24918 / 3.07 ( 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 455 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 1.102 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: 0.9144 (pptt) cc_final: 0.8693 (ptpp) REVERT: A 106 THR cc_start: 0.7238 (p) cc_final: 0.6942 (t) REVERT: B 82 GLN cc_start: 0.8422 (tt0) cc_final: 0.7710 (pt0) REVERT: B 152 ASN cc_start: 0.7587 (m-40) cc_final: 0.7381 (m110) REVERT: B 202 MET cc_start: 0.8011 (mtt) cc_final: 0.7653 (mtm) REVERT: C 76 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8835 (tm-30) REVERT: C 111 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8505 (pttm) REVERT: C 148 MET cc_start: 0.8436 (tpt) cc_final: 0.8033 (tpt) REVERT: C 209 MET cc_start: 0.7249 (mmp) cc_final: 0.6983 (mmp) REVERT: C 356 ILE cc_start: 0.9188 (pt) cc_final: 0.8652 (pt) REVERT: C 362 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7346 (mtt-85) REVERT: C 382 MET cc_start: 0.9072 (tmm) cc_final: 0.8688 (tmm) REVERT: C 383 GLU cc_start: 0.8358 (tt0) cc_final: 0.7966 (mt-10) REVERT: C 438 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8394 (mmtt) REVERT: C 587 ASP cc_start: 0.8560 (t70) cc_final: 0.8358 (t70) REVERT: C 593 MET cc_start: 0.7723 (mmm) cc_final: 0.7487 (mmm) REVERT: C 725 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6958 (tm-30) REVERT: C 1119 ASN cc_start: 0.6903 (p0) cc_final: 0.6570 (t0) REVERT: D 19 ASP cc_start: 0.8458 (t0) cc_final: 0.8137 (t70) REVERT: D 29 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8580 (mtmm) REVERT: D 154 HIS cc_start: 0.9459 (m90) cc_final: 0.9072 (m90) REVERT: D 264 ARG cc_start: 0.8658 (tpm170) cc_final: 0.8318 (tpm170) REVERT: D 296 LEU cc_start: 0.9222 (mt) cc_final: 0.8717 (mt) REVERT: D 356 ARG cc_start: 0.8373 (tpm170) cc_final: 0.8046 (tpm170) REVERT: D 373 MET cc_start: 0.7785 (tpp) cc_final: 0.7457 (tpp) REVERT: D 457 MET cc_start: 0.7266 (ttt) cc_final: 0.6868 (tpp) REVERT: D 831 ILE cc_start: 0.9263 (mt) cc_final: 0.9049 (mt) REVERT: D 843 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 919 MET cc_start: 0.7133 (mmm) cc_final: 0.6613 (mmm) REVERT: D 1191 MET cc_start: 0.8373 (pmm) cc_final: 0.8083 (pmm) REVERT: F 229 ASN cc_start: 0.8741 (t0) cc_final: 0.8233 (p0) REVERT: F 298 MET cc_start: 0.6789 (ttp) cc_final: 0.6402 (ttp) REVERT: F 342 MET cc_start: 0.7727 (ppp) cc_final: 0.7197 (ppp) REVERT: F 355 MET cc_start: 0.8258 (tpt) cc_final: 0.7740 (tpp) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.2084 time to fit residues: 151.0001 Evaluate side-chains 345 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 6.9990 chunk 287 optimal weight: 1.9990 chunk 308 optimal weight: 0.0040 chunk 154 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 317 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 200 GLN B 151 GLN ** C 529 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 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 = 0.4275 r_free = 0.4275 target = 0.133570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094184 restraints weight = 110390.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095004 restraints weight = 77709.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096167 restraints weight = 59569.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.096713 restraints weight = 45128.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096694 restraints weight = 41941.654| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 31481 Z= 0.151 Angle : 0.651 12.314 43317 Z= 0.345 Chirality : 0.046 0.346 4923 Planarity : 0.004 0.053 5067 Dihedral : 20.861 175.579 5662 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -0.09 (0.14), residues: 3458 helix: 0.82 (0.14), residues: 1404 sheet: -0.81 (0.23), residues: 435 loop : -0.53 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 810 TYR 0.030 0.002 TYR E 32 PHE 0.030 0.002 PHE A 189 TRP 0.031 0.002 TRP C 924 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (31453) covalent geometry : angle 0.64057 / 0.34 (43293) hydrogen bonds : bond 0.04288 / 3.00 ( 1408) hydrogen bonds : angle 4.47445 / 3.14 ( 3864) metal coordination : bond 0.00624 / 0.34 ( 28) metal coordination : angle 4.90586 / 2.89 ( 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 455 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.122 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: A 81 LYS cc_start: 0.9169 (pptt) cc_final: 0.8711 (ptpp) REVERT: A 106 THR cc_start: 0.7309 (p) cc_final: 0.6986 (t) REVERT: A 202 MET cc_start: 0.8430 (pmm) cc_final: 0.8083 (pmm) REVERT: B 5 GLN cc_start: 0.7962 (mp10) cc_final: 0.7652 (mp10) REVERT: B 82 GLN cc_start: 0.8417 (tt0) cc_final: 0.7693 (pt0) REVERT: C 76 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8824 (tm-30) REVERT: C 111 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8501 (pttt) REVERT: C 148 MET cc_start: 0.8559 (tpt) cc_final: 0.8112 (tpt) REVERT: C 382 MET cc_start: 0.9079 (tmm) cc_final: 0.8707 (tmm) REVERT: C 383 GLU cc_start: 0.8352 (tt0) cc_final: 0.7957 (mt-10) REVERT: C 438 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8335 (mttt) REVERT: C 725 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7100 (tm-30) REVERT: C 1053 PHE cc_start: 0.7193 (t80) cc_final: 0.6815 (t80) REVERT: C 1119 ASN cc_start: 0.6713 (p0) cc_final: 0.6476 (t0) REVERT: D 19 ASP cc_start: 0.8402 (t0) cc_final: 0.8067 (t70) REVERT: D 30 LYS cc_start: 0.9012 (tptm) cc_final: 0.8722 (tptm) REVERT: D 154 HIS cc_start: 0.9478 (m90) cc_final: 0.9078 (m90) REVERT: D 264 ARG cc_start: 0.8667 (tpm170) cc_final: 0.7947 (tpm170) REVERT: D 296 LEU cc_start: 0.9293 (mt) cc_final: 0.8798 (mt) REVERT: D 356 ARG cc_start: 0.8399 (tpm170) cc_final: 0.8057 (tpm170) REVERT: D 373 MET cc_start: 0.7579 (tpp) cc_final: 0.7348 (tpp) REVERT: D 457 MET cc_start: 0.7355 (ttt) cc_final: 0.6893 (tpp) REVERT: D 590 THR cc_start: 0.6559 (m) cc_final: 0.6346 (m) REVERT: D 808 GLN cc_start: 0.8948 (mp10) cc_final: 0.8535 (mp10) REVERT: D 809 MET cc_start: 0.8687 (ptt) cc_final: 0.8443 (ppp) REVERT: D 843 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8182 (mt-10) REVERT: D 919 MET cc_start: 0.6989 (mmm) cc_final: 0.6536 (mmm) REVERT: F 229 ASN cc_start: 0.8756 (t0) cc_final: 0.8277 (p0) REVERT: F 298 MET cc_start: 0.6833 (ttp) cc_final: 0.6455 (ttt) REVERT: F 342 MET cc_start: 0.7709 (ppp) cc_final: 0.7199 (ppp) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2095 time to fit residues: 150.9553 Evaluate side-chains 345 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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: 1.9990 chunk 242 optimal weight: 2.9990 chunk 354 optimal weight: 30.0000 chunk 253 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 232 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 151 GLN C 374 GLN ** C 529 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.133502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094968 restraints weight = 110466.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094885 restraints weight = 73320.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095967 restraints weight = 60927.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096493 restraints weight = 45657.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.096729 restraints weight = 42409.647| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31481 Z= 0.149 Angle : 0.664 16.767 43317 Z= 0.348 Chirality : 0.046 0.360 4923 Planarity : 0.005 0.069 5067 Dihedral : 20.841 175.985 5662 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.03 % Allowed : 1.34 % Favored : 98.62 % 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: 0.85 (0.14), residues: 1396 sheet: -0.76 (0.24), residues: 426 loop : -0.54 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 39 TYR 0.029 0.002 TYR E 32 PHE 0.030 0.002 PHE D1209 TRP 0.035 0.002 TRP C 924 HIS 0.006 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (31453) covalent geometry : angle 0.65181 / 0.35 (43293) hydrogen bonds : bond 0.04203 / 2.93 ( 1408) hydrogen bonds : angle 4.42006 / 3.10 ( 3864) metal coordination : bond 0.00563 / 0.28 ( 28) metal coordination : angle 5.51315 / 3.16 ( 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 451 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.040 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: A 81 LYS cc_start: 0.9188 (pptt) cc_final: 0.8709 (ptpp) REVERT: A 106 THR cc_start: 0.7361 (p) cc_final: 0.7066 (t) REVERT: A 202 MET cc_start: 0.8514 (pmm) cc_final: 0.8126 (pmm) REVERT: B 5 GLN cc_start: 0.7977 (mp10) cc_final: 0.7680 (mp10) REVERT: B 82 GLN cc_start: 0.8392 (tt0) cc_final: 0.7679 (pt0) REVERT: B 202 MET cc_start: 0.8332 (mtt) cc_final: 0.8117 (mtm) REVERT: C 111 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8489 (pttm) REVERT: C 148 MET cc_start: 0.8584 (tpt) cc_final: 0.8162 (tpt) REVERT: C 201 GLU cc_start: 0.6300 (mp0) cc_final: 0.6089 (mp0) REVERT: C 382 MET cc_start: 0.9067 (tmm) cc_final: 0.8721 (tmm) REVERT: C 383 GLU cc_start: 0.8317 (tt0) cc_final: 0.7953 (mt-10) REVERT: C 438 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8322 (mttt) REVERT: C 538 MET cc_start: 0.8622 (ttt) cc_final: 0.8268 (ttt) REVERT: C 587 ASP cc_start: 0.8648 (t0) cc_final: 0.8373 (t0) REVERT: C 725 GLN cc_start: 0.7387 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 1119 ASN cc_start: 0.6785 (p0) cc_final: 0.6523 (t0) REVERT: D 19 ASP cc_start: 0.8389 (t0) cc_final: 0.8092 (t70) REVERT: D 30 LYS cc_start: 0.9009 (tptm) cc_final: 0.8786 (tptm) REVERT: D 154 HIS cc_start: 0.9423 (m90) cc_final: 0.8998 (m90) REVERT: D 264 ARG cc_start: 0.8705 (tpm170) cc_final: 0.8363 (tpm170) REVERT: D 296 LEU cc_start: 0.9242 (mt) cc_final: 0.8709 (mt) REVERT: D 356 ARG cc_start: 0.8366 (tpm170) cc_final: 0.8070 (tpm170) REVERT: D 457 MET cc_start: 0.7280 (ttt) cc_final: 0.6826 (tpp) REVERT: D 590 THR cc_start: 0.6565 (m) cc_final: 0.6354 (m) REVERT: D 809 MET cc_start: 0.8669 (ptt) cc_final: 0.8421 (ppp) REVERT: D 831 ILE cc_start: 0.9359 (mt) cc_final: 0.9008 (mt) REVERT: D 843 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8196 (mt-10) REVERT: D 919 MET cc_start: 0.6871 (mmm) cc_final: 0.6446 (mmm) REVERT: D 1191 MET cc_start: 0.8427 (pmm) cc_final: 0.8210 (pmm) REVERT: F 229 ASN cc_start: 0.8669 (t0) cc_final: 0.8249 (p0) REVERT: F 298 MET cc_start: 0.6869 (ttp) cc_final: 0.6460 (ttt) REVERT: F 342 MET cc_start: 0.7715 (ppp) cc_final: 0.7203 (ppp) REVERT: F 355 MET cc_start: 0.8216 (tpt) cc_final: 0.7746 (tpp) outliers start: 1 outliers final: 1 residues processed: 451 average time/residue: 0.2079 time to fit residues: 149.9287 Evaluate side-chains 347 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 0.9980 chunk 171 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 316 optimal weight: 0.9980 chunk 348 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 200 GLN B 151 GLN ** C 529 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 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 = 0.4268 r_free = 0.4268 target = 0.133046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093548 restraints weight = 110584.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094515 restraints weight = 78394.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094874 restraints weight = 59201.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095770 restraints weight = 48814.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095784 restraints weight = 41982.431| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31481 Z= 0.161 Angle : 0.673 17.279 43317 Z= 0.353 Chirality : 0.046 0.334 4923 Planarity : 0.004 0.055 5067 Dihedral : 20.814 176.401 5662 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.89 (0.14), residues: 1389 sheet: -0.73 (0.24), residues: 429 loop : -0.56 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 810 TYR 0.029 0.002 TYR E 32 PHE 0.027 0.002 PHE D1209 TRP 0.048 0.003 TRP C1059 HIS 0.007 0.001 HIS D 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (31453) covalent geometry : angle 0.65830 / 0.35 (43293) hydrogen bonds : bond 0.04217 / 2.93 ( 1408) hydrogen bonds : angle 4.47094 / 3.14 ( 3864) metal coordination : bond 0.00617 / 0.26 ( 28) metal coordination : angle 6.05801 / 3.55 ( 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 446 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.103 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 81 LYS cc_start: 0.9197 (pptt) cc_final: 0.8707 (ptpp) REVERT: A 95 MET cc_start: 0.8118 (ttm) cc_final: 0.7582 (tpp) REVERT: A 106 THR cc_start: 0.7138 (p) cc_final: 0.6764 (t) REVERT: A 202 MET cc_start: 0.8488 (pmm) cc_final: 0.8103 (pmm) REVERT: B 5 GLN cc_start: 0.7859 (mp10) cc_final: 0.7604 (mp10) REVERT: B 82 GLN cc_start: 0.8463 (tt0) cc_final: 0.7758 (pt0) REVERT: C 76 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 148 MET cc_start: 0.8594 (tpt) cc_final: 0.8176 (tpt) REVERT: C 201 GLU cc_start: 0.6693 (mp0) cc_final: 0.6367 (mp0) REVERT: C 246 MET cc_start: 0.9171 (ppp) cc_final: 0.8742 (ppp) REVERT: C 382 MET cc_start: 0.9042 (tmm) cc_final: 0.8710 (tmm) REVERT: C 383 GLU cc_start: 0.8318 (tt0) cc_final: 0.7872 (mt-10) REVERT: C 538 MET cc_start: 0.8608 (ttt) cc_final: 0.8312 (ttt) REVERT: C 587 ASP cc_start: 0.8692 (t0) cc_final: 0.8396 (t0) REVERT: C 593 MET cc_start: 0.8023 (mmm) cc_final: 0.7768 (mmm) REVERT: C 725 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7095 (tm-30) REVERT: C 1053 PHE cc_start: 0.7134 (t80) cc_final: 0.6883 (t80) REVERT: C 1119 ASN cc_start: 0.6857 (p0) cc_final: 0.6535 (t0) REVERT: D 19 ASP cc_start: 0.8463 (t0) cc_final: 0.8144 (t0) REVERT: D 30 LYS cc_start: 0.9016 (tptm) cc_final: 0.8812 (tptm) REVERT: D 154 HIS cc_start: 0.9467 (m90) cc_final: 0.9029 (m90) REVERT: D 264 ARG cc_start: 0.8694 (tpm170) cc_final: 0.8025 (tpm170) REVERT: D 296 LEU cc_start: 0.9270 (mt) cc_final: 0.8785 (mt) REVERT: D 327 MET cc_start: 0.8103 (ttm) cc_final: 0.7890 (ttm) REVERT: D 356 ARG cc_start: 0.8399 (tpm170) cc_final: 0.8091 (tpm170) REVERT: D 405 MET cc_start: 0.7996 (tpp) cc_final: 0.7600 (mmt) REVERT: D 457 MET cc_start: 0.7335 (ttt) cc_final: 0.6923 (tpp) REVERT: D 808 GLN cc_start: 0.8780 (mp10) cc_final: 0.8144 (mp10) REVERT: D 831 ILE cc_start: 0.9349 (mt) cc_final: 0.9044 (mt) REVERT: D 843 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 919 MET cc_start: 0.6907 (mmm) cc_final: 0.6479 (mmm) REVERT: E 79 LEU cc_start: 0.8501 (mp) cc_final: 0.7758 (tt) REVERT: F 229 ASN cc_start: 0.8801 (t0) cc_final: 0.8272 (p0) REVERT: F 298 MET cc_start: 0.6939 (ttp) cc_final: 0.6507 (ttt) REVERT: F 342 MET cc_start: 0.7746 (ppp) cc_final: 0.7306 (ppp) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2063 time to fit residues: 147.0375 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 : 1.087 ------------------------------------------------------------------------------- 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: 2.9990 chunk 163 optimal weight: 0.0270 chunk 175 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 327 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 89 HIS B 151 GLN ** C 529 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 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 = 0.4269 r_free = 0.4269 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093350 restraints weight = 110208.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094942 restraints weight = 75253.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095133 restraints weight = 54684.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095701 restraints weight = 48947.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095613 restraints weight = 42850.756| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31481 Z= 0.155 Angle : 0.669 16.139 43317 Z= 0.349 Chirality : 0.046 0.331 4923 Planarity : 0.005 0.081 5067 Dihedral : 20.778 176.868 5662 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1392 sheet: -0.81 (0.24), residues: 436 loop : -0.53 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 810 TYR 0.030 0.002 TYR E 32 PHE 0.027 0.002 PHE D1209 TRP 0.046 0.002 TRP C 924 HIS 0.004 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (31453) covalent geometry : angle 0.65619 / 0.35 (43293) hydrogen bonds : bond 0.04162 / 2.89 ( 1408) hydrogen bonds : angle 4.44851 / 3.12 ( 3864) metal coordination : bond 0.00667 / 0.31 ( 28) metal coordination : angle 5.66638 / 3.37 ( 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 439 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.137 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: A 95 MET cc_start: 0.8104 (ttm) cc_final: 0.7630 (tpp) REVERT: A 106 THR cc_start: 0.7093 (p) cc_final: 0.6749 (t) REVERT: A 134 LEU cc_start: 0.8934 (tp) cc_final: 0.8411 (tp) REVERT: A 202 MET cc_start: 0.8492 (pmm) cc_final: 0.8105 (pmm) REVERT: B 5 GLN cc_start: 0.7948 (mp10) cc_final: 0.7687 (mp10) REVERT: B 82 GLN cc_start: 0.8480 (tt0) cc_final: 0.7767 (pt0) REVERT: C 76 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 148 MET cc_start: 0.8608 (tpt) cc_final: 0.8336 (tpt) REVERT: C 246 MET cc_start: 0.9177 (ppp) cc_final: 0.8744 (ppp) REVERT: C 382 MET cc_start: 0.9040 (tmm) cc_final: 0.8730 (tmm) REVERT: C 383 GLU cc_start: 0.8337 (tt0) cc_final: 0.7889 (mt-10) REVERT: C 538 MET cc_start: 0.8590 (ttt) cc_final: 0.8172 (ttt) REVERT: C 593 MET cc_start: 0.8022 (mmm) cc_final: 0.7772 (mmm) REVERT: C 992 LYS cc_start: 0.6579 (mmtt) cc_final: 0.5732 (mmmt) REVERT: C 1119 ASN cc_start: 0.6885 (p0) cc_final: 0.6515 (t0) REVERT: D 19 ASP cc_start: 0.8457 (t0) cc_final: 0.8138 (t0) REVERT: D 30 LYS cc_start: 0.9009 (tptm) cc_final: 0.8803 (tptm) REVERT: D 264 ARG cc_start: 0.8728 (tpm170) cc_final: 0.7978 (tpm170) REVERT: D 296 LEU cc_start: 0.9343 (mt) cc_final: 0.8822 (mt) REVERT: D 352 ASN cc_start: 0.8511 (m-40) cc_final: 0.8273 (m110) REVERT: D 356 ARG cc_start: 0.8370 (tpm170) cc_final: 0.8008 (tpm170) REVERT: D 405 MET cc_start: 0.7963 (tpp) cc_final: 0.7512 (mmt) REVERT: D 457 MET cc_start: 0.7219 (ttt) cc_final: 0.6820 (tpp) REVERT: D 590 THR cc_start: 0.6766 (m) cc_final: 0.6542 (m) REVERT: D 745 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 808 GLN cc_start: 0.8812 (mp10) cc_final: 0.8507 (mp10) REVERT: D 831 ILE cc_start: 0.9349 (mt) cc_final: 0.9078 (mt) REVERT: D 919 MET cc_start: 0.6898 (mmm) cc_final: 0.6481 (mmm) REVERT: D 971 MET cc_start: 0.8094 (ppp) cc_final: 0.7880 (ppp) REVERT: D 1028 GLU cc_start: 0.8268 (tt0) cc_final: 0.8062 (tt0) REVERT: E 79 LEU cc_start: 0.8405 (mp) cc_final: 0.7667 (tt) REVERT: F 229 ASN cc_start: 0.8799 (t0) cc_final: 0.8237 (p0) REVERT: F 298 MET cc_start: 0.6945 (ttp) cc_final: 0.6502 (ttt) REVERT: F 342 MET cc_start: 0.7732 (ppp) cc_final: 0.7304 (ppp) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.2006 time to fit residues: 141.6622 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 : 1.070 ------------------------------------------------------------------------------- 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: 6.9990 chunk 300 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 243 optimal weight: 0.4980 chunk 342 optimal weight: 50.0000 chunk 287 optimal weight: 1.9990 chunk 220 optimal weight: 0.3980 chunk 205 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 137 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.133985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095151 restraints weight = 110461.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.096221 restraints weight = 75125.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096344 restraints weight = 57579.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097160 restraints weight = 49676.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097157 restraints weight = 43288.605| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31481 Z= 0.129 Angle : 0.656 14.589 43317 Z= 0.341 Chirality : 0.045 0.411 4923 Planarity : 0.004 0.053 5067 Dihedral : 20.728 177.052 5662 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.04 (0.14), residues: 3458 helix: 0.95 (0.14), residues: 1392 sheet: -0.73 (0.24), residues: 426 loop : -0.49 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 746 TYR 0.015 0.001 TYR C1064 PHE 0.024 0.002 PHE D1209 TRP 0.045 0.002 TRP C 924 HIS 0.004 0.001 HIS D 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (31453) covalent geometry : angle 0.64398 / 0.34 (43293) hydrogen bonds : bond 0.04060 / 2.83 ( 1408) hydrogen bonds : angle 4.34701 / 3.05 ( 3864) metal coordination : bond 0.00487 / 0.24 ( 28) metal coordination : angle 5.29462 / 3.16 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5733.44 seconds wall clock time: 100 minutes 4.30 seconds (6004.30 seconds total)