Starting phenix.real_space_refine (version: dev) on Mon Feb 27 16:17:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2023/7vpz_32077_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2023/7vpz_32077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2023/7vpz_32077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2023/7vpz_32077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2023/7vpz_32077_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpz_32077/02_2023/7vpz_32077_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A GLU 184": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C ASP 587": "OD1" <-> "OD2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C GLU 739": "OE1" <-> "OE2" Residue "C GLU 888": "OE1" <-> "OE2" Residue "C PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1095": "OE1" <-> "OE2" Residue "C GLU 1112": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 837": "OE1" <-> "OE2" Residue "D GLU 843": "OE1" <-> "OE2" Residue "D GLU 884": "OE1" <-> "OE2" Residue "D PHE 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "F GLU 426": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: 17.22, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 14.02 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 24 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6402 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 43 sheets defined 44.1% alpha, 13.9% beta 65 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 10.25 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: 17.10 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9417 1.34 - 1.46: 5296 1.46 - 1.58: 16223 1.58 - 1.70: 342 1.70 - 1.82: 175 Bond restraints: 31453 Sorted by residual: bond pdb=" CA GLN C1040 " pdb=" C GLN C1040 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" O3' DG O 71 " pdb=" P DG O 72 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 1.00e+01 bond pdb=" C1' DG P 15 " pdb=" N9 DG P 15 " ideal model delta sigma weight residual 1.460 1.402 0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.81e+00 bond pdb=" N ALA D 133 " pdb=" CA ALA D 133 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.44e+00 ... (remaining 31448 not shown) Histogram of bond angle deviations from ideal: 97.64 - 105.21: 1193 105.21 - 112.78: 16970 112.78 - 120.35: 12964 120.35 - 127.91: 11680 127.91 - 135.48: 486 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: 17706 35.45 - 70.89: 859 70.89 - 106.34: 30 106.34 - 141.78: 4 141.78 - 177.23: 14 Dihedral angle restraints: 18613 sinusoidal: 8667 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 18610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4637 0.098 - 0.196: 264 0.196 - 0.294: 19 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 4923 Sorted by residual: chirality pdb=" CA LYS D 823 " pdb=" N LYS D 823 " pdb=" C LYS D 823 " pdb=" CB LYS D 823 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA GLN C1039 " pdb=" N GLN C1039 " pdb=" C GLN C1039 " pdb=" CB GLN C1039 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ARG C 293 " pdb=" N ARG C 293 " pdb=" C ARG C 293 " pdb=" CB ARG C 293 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 4920 not shown) Planarity restraints: 5067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 443 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO D 444 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 444 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 444 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1059 " 0.009 2.00e-02 2.50e+03 1.51e-02 5.74e+00 pdb=" CG TRP C1059 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C1059 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C1059 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C1059 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C1059 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1059 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1059 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1059 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1059 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 738 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LYS D 738 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS D 738 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 739 " 0.013 2.00e-02 2.50e+03 ... (remaining 5064 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 202 2.49 - 3.09: 23379 3.09 - 3.69: 50724 3.69 - 4.30: 69675 4.30 - 4.90: 108837 Nonbonded interactions: 252817 Sorted by model distance: nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.887 2.230 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.903 2.230 nonbonded pdb=" O3' G Q 5 " pdb="MG MG D1401 " model vdw 1.974 2.170 nonbonded pdb=" OE2 GLU M 105 " pdb="ZN ZN M 203 " model vdw 2.066 2.230 nonbonded pdb=" OG1 THR C 339 " pdb=" OE1 GLU C 340 " model vdw 2.107 2.440 ... (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 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 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. 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.050 Check model and map are aligned: 0.460 Process input model: 98.140 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.320 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.990 ------------------------------------------------------------------------------- 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 0.058 31453 Z= 0.288 Angle : 0.786 13.742 43293 Z= 0.458 Chirality : 0.049 0.490 4923 Planarity : 0.005 0.063 5067 Dihedral : 18.569 177.230 12211 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 543 time to evaluate : 3.260 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 outliers start: 15 outliers final: 1 residues processed: 553 average time/residue: 0.4635 time to fit residues: 393.4249 Evaluate side-chains 387 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 386 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2621 time to fit residues: 5.1204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 326 optimal weight: 50.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 152 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 921 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN D 510 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 HIS D 669 ASN D 778 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 ASN F 282 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 31453 Z= 0.323 Angle : 0.688 8.168 43293 Z= 0.372 Chirality : 0.044 0.211 4923 Planarity : 0.005 0.060 5067 Dihedral : 20.848 179.764 5530 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3458 helix: 0.84 (0.13), residues: 1401 sheet: -0.78 (0.25), residues: 403 loop : -0.75 (0.15), residues: 1654 *********************** 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 484 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 479 time to evaluate : 3.065 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 outliers start: 5 outliers final: 1 residues processed: 484 average time/residue: 0.4810 time to fit residues: 359.8087 Evaluate side-chains 352 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 3.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2482 time to fit residues: 4.6686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 272 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 327 optimal weight: 50.0000 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 0.9980 chunk 324 optimal weight: 50.0000 chunk 111 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 465 HIS ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN D 778 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 31453 Z= 0.307 Angle : 0.671 8.512 43293 Z= 0.362 Chirality : 0.044 0.200 4923 Planarity : 0.005 0.074 5067 Dihedral : 20.815 179.904 5530 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3458 helix: 0.71 (0.13), residues: 1406 sheet: -0.81 (0.24), residues: 399 loop : -0.88 (0.14), residues: 1653 *********************** 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 460 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 457 time to evaluate : 2.523 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 outliers start: 3 outliers final: 1 residues processed: 460 average time/residue: 0.4480 time to fit residues: 318.2350 Evaluate side-chains 344 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 3.227 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2573 time to fit residues: 4.8889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 20.0000 chunk 246 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 328 optimal weight: 30.0000 chunk 347 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1182 HIS ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 31453 Z= 0.263 Angle : 0.640 11.646 43293 Z= 0.343 Chirality : 0.043 0.229 4923 Planarity : 0.004 0.055 5067 Dihedral : 20.765 179.045 5530 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3458 helix: 0.83 (0.14), residues: 1405 sheet: -0.89 (0.24), residues: 422 loop : -0.81 (0.15), residues: 1631 *********************** 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 445 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 3.649 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 outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.4888 time to fit residues: 339.4612 Evaluate side-chains 340 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 3.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 HIS ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN C 361 ASN C 741 HIS ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 ASN D 792 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 31453 Z= 0.325 Angle : 0.684 9.217 43293 Z= 0.364 Chirality : 0.044 0.222 4923 Planarity : 0.005 0.078 5067 Dihedral : 20.794 179.866 5530 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3458 helix: 0.69 (0.13), residues: 1412 sheet: -0.87 (0.24), residues: 423 loop : -0.90 (0.15), residues: 1623 *********************** 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 428 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 3.564 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 outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.4767 time to fit residues: 320.7075 Evaluate side-chains 329 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 3.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 31453 Z= 0.339 Angle : 0.687 9.476 43293 Z= 0.367 Chirality : 0.044 0.260 4923 Planarity : 0.005 0.065 5067 Dihedral : 20.824 179.814 5530 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3458 helix: 0.64 (0.14), residues: 1398 sheet: -0.89 (0.25), residues: 406 loop : -0.90 (0.15), residues: 1654 *********************** 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 417 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 3.280 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 outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.4956 time to fit residues: 321.4317 Evaluate side-chains 314 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 3.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 chunk 198 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 217 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 778 ASN ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 31453 Z= 0.194 Angle : 0.625 11.651 43293 Z= 0.330 Chirality : 0.042 0.202 4923 Planarity : 0.004 0.048 5067 Dihedral : 20.692 179.914 5530 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3458 helix: 0.93 (0.14), residues: 1385 sheet: -0.81 (0.24), residues: 424 loop : -0.73 (0.15), residues: 1649 *********************** 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 446 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 3.294 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 outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.4683 time to fit residues: 329.8415 Evaluate side-chains 329 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 3.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3084 ------------------------------------------------------------------------------- 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: 3.9990 chunk 138 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 220 optimal weight: 0.0770 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN B 151 GLN C 374 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 31453 Z= 0.201 Angle : 0.628 9.204 43293 Z= 0.330 Chirality : 0.042 0.282 4923 Planarity : 0.004 0.050 5067 Dihedral : 20.600 179.606 5530 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3458 helix: 1.03 (0.14), residues: 1385 sheet: -0.75 (0.24), residues: 416 loop : -0.69 (0.15), residues: 1657 *********************** 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 437 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.121 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 outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.4783 time to fit residues: 330.6177 Evaluate side-chains 328 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 3.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 303 optimal weight: 0.9980 chunk 323 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 253 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN C 462 HIS ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 31453 Z= 0.259 Angle : 0.655 9.443 43293 Z= 0.346 Chirality : 0.043 0.282 4923 Planarity : 0.005 0.057 5067 Dihedral : 20.588 179.135 5530 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3458 helix: 0.93 (0.14), residues: 1397 sheet: -0.74 (0.24), residues: 413 loop : -0.75 (0.15), residues: 1648 *********************** 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 425 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.389 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 outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.4786 time to fit residues: 317.9488 Evaluate side-chains 319 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 3.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.5980 chunk 341 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 0.0870 chunk 358 optimal weight: 30.0000 chunk 330 optimal weight: 50.0000 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 31453 Z= 0.293 Angle : 0.685 11.909 43293 Z= 0.362 Chirality : 0.044 0.300 4923 Planarity : 0.005 0.054 5067 Dihedral : 20.565 178.796 5530 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3458 helix: 0.83 (0.14), residues: 1405 sheet: -0.67 (0.26), residues: 385 loop : -0.83 (0.15), residues: 1668 ********************** 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 413 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 3.364 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 outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.4899 time to fit residues: 318.5318 Evaluate side-chains 313 residues out of total 2910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.130859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093674 restraints weight = 112704.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093532 restraints weight = 79627.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094140 restraints weight = 58712.266| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 31453 Z= 0.206 Angle : 0.647 10.207 43293 Z= 0.339 Chirality : 0.043 0.276 4923 Planarity : 0.004 0.056 5067 Dihedral : 20.519 178.772 5530 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3458 helix: 0.96 (0.14), residues: 1398 sheet: -0.71 (0.26), residues: 399 loop : -0.72 (0.15), residues: 1661 =============================================================================== Job complete usr+sys time: 6486.28 seconds wall clock time: 122 minutes 44.49 seconds (7364.49 seconds total)