Starting phenix.real_space_refine on Sat Apr 13 18:56:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pyk_13718/04_2024/7pyk_13718.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pyk_13718/04_2024/7pyk_13718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pyk_13718/04_2024/7pyk_13718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pyk_13718/04_2024/7pyk_13718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pyk_13718/04_2024/7pyk_13718.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pyk_13718/04_2024/7pyk_13718.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 67 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18081 2.51 5 N 5263 2.21 5 O 5823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 174": "OD1" <-> "OD2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C GLU 775": "OE1" <-> "OE2" Residue "C TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1241": "OD1" <-> "OD2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1279": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 987": "OE1" <-> "OE2" Residue "D PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1305": "OD1" <-> "OD2" Residue "D GLU 1334": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29342 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2076 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 56, 'TRANS': 1282} Chain: "D" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10375 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 830 Chain: "N" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14877 SG CYS D 70 107.767 126.019 80.965 1.00309.02 S ATOM 14891 SG CYS D 72 107.057 128.885 81.697 1.00300.42 S ATOM 20711 SG CYS D 814 118.669 64.937 110.080 1.00205.05 S ATOM 21327 SG CYS D 895 117.921 66.665 107.635 1.00198.23 S ATOM 21348 SG CYS D 898 115.751 63.769 108.194 1.00190.15 S Time building chain proxies: 16.05, per 1000 atoms: 0.55 Number of scatterers: 29342 At special positions: 0 Unit cell: (190.75, 152.6, 184.21, 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 2 29.99 S 105 16.00 P 67 15.00 Mg 1 11.99 O 5823 8.00 N 5263 7.00 C 18081 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: 12.72 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 50 sheets defined 39.6% alpha, 13.5% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 9.67 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.540A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.514A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.768A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.989A pdb=" N ASP B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 260 " --> pdb=" O VAL B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 260' Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.476A pdb=" N ASN B 268 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 296 through 309 removed outlier: 3.615A pdb=" N LYS B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.994A pdb=" N ALA B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.737A pdb=" N GLN C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.551A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.621A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.585A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.663A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.707A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 4.150A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.512A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.036A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.674A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.592A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.418A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 4.183A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.679A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.935A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.333A pdb=" N ARG C 903 " --> pdb=" O GLU C 899 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.326A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.577A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.582A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.563A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 3.667A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.643A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.512A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.588A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.543A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.760A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.161A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 173 through 176 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.738A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.141A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.988A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.064A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.545A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.683A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.795A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.581A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.644A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.892A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.624A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.554A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.561A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.586A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.509A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.914A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.531A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.866A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D1260 " --> pdb=" O ILE D1256 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.507A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.608A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 3.855A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.663A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.829A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 21 through 39 removed outlier: 3.639A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.818A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 5.884A pdb=" N ARG F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 84 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 131 removed outlier: 4.488A pdb=" N VAL F 115 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN F 116 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 207 through 211 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 281 through 287 Processing helix chain 'F' and resid 314 through 319 removed outlier: 4.015A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 333 removed outlier: 3.508A pdb=" N SER F 329 " --> pdb=" O VAL F 325 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 353 removed outlier: 4.069A pdb=" N ALA F 352 " --> pdb=" O GLN F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 391 through 395 removed outlier: 4.459A pdb=" N GLU F 394 " --> pdb=" O GLU F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.576A pdb=" N ALA F 405 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU F 406 " --> pdb=" O VAL F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 402 through 406' Processing helix chain 'F' and resid 408 through 417 removed outlier: 3.821A pdb=" N ASN F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 441 through 447 Processing helix chain 'F' and resid 448 through 452 removed outlier: 4.037A pdb=" N ARG F 451 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY F 452 " --> pdb=" O ALA F 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 448 through 452' Processing helix chain 'F' and resid 455 through 460 removed outlier: 3.549A pdb=" N LEU F 459 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 455 through 460' Processing helix chain 'F' and resid 475 through 480 removed outlier: 4.377A pdb=" N ALA F 480 " --> pdb=" O GLU F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 487 Processing helix chain 'F' and resid 487 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15 removed outlier: 7.286A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 7.142A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.918A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.745A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.691A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 58 removed outlier: 7.228A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.079A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.522A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.144A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.917A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 removed outlier: 4.190A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 335 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 333 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 251 removed outlier: 4.032A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.787A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.976A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.918A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.500A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.746A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.051A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.852A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.602A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.602A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.223A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.508A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 547 through 549 Processing sheet with id=AE1, first strand: chain 'D' and resid 553 through 556 Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 709 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.159A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.419A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.615A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1049 Processing sheet with id=AE9, first strand: chain 'D' and resid 1186 through 1190 removed outlier: 3.997A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D1176 " --> pdb=" O PHE D1165 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE D1165 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR D1178 " --> pdb=" O VAL D1163 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D1163 " --> pdb=" O THR D1178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 5.364A pdb=" N ILE D1266 " --> pdb=" O SER D1303 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER D1303 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN D1268 " --> pdb=" O THR D1301 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AF3, first strand: chain 'F' and resid 138 through 141 Processing sheet with id=AF4, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.450A pdb=" N GLU F 159 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 296 through 299 removed outlier: 3.749A pdb=" N ASP F 299 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR F 304 " --> pdb=" O ASP F 299 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 14.76 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6728 1.33 - 1.45: 6018 1.45 - 1.57: 16809 1.57 - 1.70: 131 1.70 - 1.82: 182 Bond restraints: 29868 Sorted by residual: bond pdb=" C PHE C 57 " pdb=" N PRO C 58 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.12e-02 7.97e+03 7.80e+00 bond pdb=" N LEU B 13 " pdb=" CA LEU B 13 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.42e-02 4.96e+03 4.49e+00 bond pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.91e+00 bond pdb=" CB GLN D 921 " pdb=" CG GLN D 921 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.51e+00 bond pdb=" CB MET C 369 " pdb=" CG MET C 369 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 ... (remaining 29863 not shown) Histogram of bond angle deviations from ideal: 95.68 - 103.37: 427 103.37 - 111.05: 11493 111.05 - 118.73: 12690 118.73 - 126.42: 15735 126.42 - 134.10: 403 Bond angle restraints: 40748 Sorted by residual: angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 112.12 107.32 4.80 8.40e-01 1.42e+00 3.27e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 130.32 -8.62 1.80e+00 3.09e-01 2.29e+01 angle pdb=" N VAL C 56 " pdb=" CA VAL C 56 " pdb=" C VAL C 56 " ideal model delta sigma weight residual 113.10 108.52 4.58 9.70e-01 1.06e+00 2.23e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 129.79 -8.09 1.80e+00 3.09e-01 2.02e+01 angle pdb=" C LEU D 252 " pdb=" N VAL D 253 " pdb=" CA VAL D 253 " ideal model delta sigma weight residual 123.33 119.46 3.87 8.70e-01 1.32e+00 1.98e+01 ... (remaining 40743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.55: 17318 29.55 - 59.10: 763 59.10 - 88.65: 69 88.65 - 118.21: 3 118.21 - 147.76: 5 Dihedral angle restraints: 18158 sinusoidal: 7278 harmonic: 10880 Sorted by residual: dihedral pdb=" CA GLY D 318 " pdb=" C GLY D 318 " pdb=" N SER D 319 " pdb=" CA SER D 319 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLU B 319 " pdb=" C GLU B 319 " pdb=" N ASN B 320 " pdb=" CA ASN B 320 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 18155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3325 0.045 - 0.090: 1054 0.090 - 0.135: 337 0.135 - 0.180: 32 0.180 - 0.226: 4 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CB ILE A 16 " pdb=" CA ILE A 16 " pdb=" CG1 ILE A 16 " pdb=" CG2 ILE A 16 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR D 48 " pdb=" CA THR D 48 " pdb=" OG1 THR D 48 " pdb=" CG2 THR D 48 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLU D1146 " pdb=" N GLU D1146 " pdb=" C GLU D1146 " pdb=" CB GLU D1146 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4749 not shown) Planarity restraints: 5163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 686 " -0.021 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP D 686 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP D 686 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 686 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 686 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 686 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 686 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 686 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 686 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP D 686 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 563 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO C 564 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 564 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 564 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C1184 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO C1185 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C1185 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C1185 " 0.034 5.00e-02 4.00e+02 ... (remaining 5160 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 12 2.19 - 2.87: 10739 2.87 - 3.54: 44486 3.54 - 4.22: 67574 4.22 - 4.90: 109903 Nonbonded interactions: 232714 Sorted by model distance: nonbonded pdb=" NH2 ARG D 883 " pdb=" SG CYS D 898 " model vdw 1.512 2.880 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.027 2.310 nonbonded pdb=" N2 DG N 37 " pdb=" O2 DC T 3 " model vdw 2.086 2.496 nonbonded pdb=" OG1 THR D1169 " pdb=" O LYS D1172 " model vdw 2.136 2.440 nonbonded pdb=" NH2 ARG D 883 " pdb="ZN ZN D1503 " model vdw 2.140 2.310 ... (remaining 232709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.020 Extract box with map and model: 6.160 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 94.050 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29868 Z= 0.258 Angle : 0.769 12.723 40748 Z= 0.421 Chirality : 0.048 0.226 4752 Planarity : 0.005 0.062 5163 Dihedral : 15.730 147.756 11140 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.75 (0.13), residues: 3767 helix: -0.30 (0.14), residues: 1255 sheet: -1.23 (0.25), residues: 423 loop : -1.71 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP D 686 HIS 0.009 0.001 HIS C 150 PHE 0.026 0.002 PHE C 186 TYR 0.023 0.001 TYR A 68 ARG 0.008 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 3.571 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: A 142 MET cc_start: 0.9438 (pmm) cc_final: 0.9055 (pmm) REVERT: A 177 TYR cc_start: 0.7630 (m-10) cc_final: 0.7295 (m-10) REVERT: B 214 GLU cc_start: 0.8687 (tt0) cc_final: 0.7825 (tp30) REVERT: C 403 MET cc_start: 0.9407 (tmm) cc_final: 0.9105 (tmm) REVERT: C 459 MET cc_start: 0.9555 (mmp) cc_final: 0.9320 (mmp) REVERT: C 515 MET cc_start: 0.7658 (ptm) cc_final: 0.7263 (ptp) REVERT: C 549 ASP cc_start: 0.9360 (t0) cc_final: 0.9048 (t0) REVERT: C 653 MET cc_start: 0.8806 (tpt) cc_final: 0.8540 (tpt) REVERT: C 681 MET cc_start: 0.9429 (mmp) cc_final: 0.9213 (mmp) REVERT: C 704 MET cc_start: 0.9452 (mmp) cc_final: 0.9230 (mmp) REVERT: C 764 CYS cc_start: 0.9461 (t) cc_final: 0.9252 (t) REVERT: C 805 MET cc_start: 0.8763 (ppp) cc_final: 0.8285 (ppp) REVERT: C 865 LEU cc_start: 0.9304 (mt) cc_final: 0.8966 (mt) REVERT: C 883 LEU cc_start: 0.8884 (mp) cc_final: 0.8636 (mp) REVERT: C 951 MET cc_start: 0.9233 (mmp) cc_final: 0.8966 (mmm) REVERT: C 1066 MET cc_start: 0.8857 (tpp) cc_final: 0.8571 (tpp) REVERT: C 1108 ASN cc_start: 0.9442 (m-40) cc_final: 0.8900 (t0) REVERT: C 1114 GLU cc_start: 0.9553 (tm-30) cc_final: 0.9233 (tm-30) REVERT: C 1232 MET cc_start: 0.9153 (mmm) cc_final: 0.8896 (mmm) REVERT: C 1273 MET cc_start: 0.9313 (mmp) cc_final: 0.8481 (mmm) REVERT: D 29 MET cc_start: 0.9374 (tmm) cc_final: 0.9134 (ppp) REVERT: D 245 LEU cc_start: 0.9337 (tp) cc_final: 0.9089 (tp) REVERT: D 265 LEU cc_start: 0.9856 (mp) cc_final: 0.9590 (pp) REVERT: D 329 ASP cc_start: 0.8980 (m-30) cc_final: 0.8714 (m-30) REVERT: D 330 MET cc_start: 0.9336 (tpt) cc_final: 0.8735 (tpp) REVERT: D 355 ILE cc_start: 0.9660 (tp) cc_final: 0.9459 (tp) REVERT: D 454 CYS cc_start: 0.9330 (m) cc_final: 0.9105 (m) REVERT: D 484 MET cc_start: 0.8724 (mpp) cc_final: 0.8466 (mpp) REVERT: D 485 MET cc_start: 0.9007 (mmp) cc_final: 0.7962 (mmm) REVERT: D 544 LEU cc_start: 0.8813 (tt) cc_final: 0.8410 (tp) REVERT: D 644 MET cc_start: 0.9394 (mpp) cc_final: 0.9078 (mpp) REVERT: D 698 MET cc_start: 0.9183 (tmm) cc_final: 0.8726 (tmm) REVERT: D 720 ASN cc_start: 0.9296 (t0) cc_final: 0.9034 (t0) REVERT: D 725 MET cc_start: 0.9524 (tpp) cc_final: 0.8775 (tpt) REVERT: D 982 LEU cc_start: 0.9742 (tp) cc_final: 0.9398 (pt) REVERT: D 1143 ASP cc_start: 0.9236 (p0) cc_final: 0.8918 (t0) REVERT: D 1186 TYR cc_start: 0.9038 (m-10) cc_final: 0.8696 (m-10) REVERT: E 18 ASP cc_start: 0.9473 (m-30) cc_final: 0.9225 (t70) REVERT: E 26 ARG cc_start: 0.9579 (tpm170) cc_final: 0.8993 (tpm170) REVERT: E 56 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8973 (tm-30) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.3728 time to fit residues: 158.3591 Evaluate side-chains 184 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 10.0000 chunk 289 optimal weight: 40.0000 chunk 160 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 299 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 346 optimal weight: 30.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29868 Z= 0.243 Angle : 0.606 9.223 40748 Z= 0.327 Chirality : 0.043 0.166 4752 Planarity : 0.005 0.056 5163 Dihedral : 14.925 149.333 4863 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.47 (0.13), residues: 3767 helix: 0.06 (0.14), residues: 1319 sheet: -1.32 (0.23), residues: 485 loop : -1.61 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 686 HIS 0.006 0.001 HIS C 150 PHE 0.015 0.002 PHE C 186 TYR 0.012 0.001 TYR D 795 ARG 0.004 0.000 ARG C1211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 3.422 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: A 142 MET cc_start: 0.9363 (pmm) cc_final: 0.8968 (pmm) REVERT: A 177 TYR cc_start: 0.7377 (m-10) cc_final: 0.6972 (m-10) REVERT: C 35 PHE cc_start: 0.9256 (t80) cc_final: 0.9047 (t80) REVERT: C 85 CYS cc_start: 0.9521 (m) cc_final: 0.9309 (m) REVERT: C 403 MET cc_start: 0.9341 (tmm) cc_final: 0.9065 (tmm) REVERT: C 515 MET cc_start: 0.7727 (ptm) cc_final: 0.7202 (ptp) REVERT: C 516 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7058 (p0) REVERT: C 549 ASP cc_start: 0.9366 (t0) cc_final: 0.9069 (t0) REVERT: C 653 MET cc_start: 0.8651 (tpt) cc_final: 0.8273 (tpt) REVERT: C 704 MET cc_start: 0.9475 (mmp) cc_final: 0.9247 (mmp) REVERT: C 794 LEU cc_start: 0.9664 (tt) cc_final: 0.9245 (pp) REVERT: C 805 MET cc_start: 0.8773 (ppp) cc_final: 0.8303 (ppp) REVERT: C 865 LEU cc_start: 0.9283 (mt) cc_final: 0.9036 (mt) REVERT: C 951 MET cc_start: 0.9211 (mmp) cc_final: 0.8892 (mmm) REVERT: C 1114 GLU cc_start: 0.9550 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 1230 MET cc_start: 0.8721 (tpt) cc_final: 0.8460 (tpp) REVERT: D 120 LEU cc_start: 0.9527 (mt) cc_final: 0.9095 (tp) REVERT: D 130 MET cc_start: 0.7738 (ppp) cc_final: 0.7490 (ppp) REVERT: D 180 MET cc_start: 0.8222 (ppp) cc_final: 0.7787 (ppp) REVERT: D 245 LEU cc_start: 0.9294 (tp) cc_final: 0.9026 (tp) REVERT: D 265 LEU cc_start: 0.9855 (mp) cc_final: 0.9619 (pp) REVERT: D 329 ASP cc_start: 0.9121 (m-30) cc_final: 0.8851 (m-30) REVERT: D 330 MET cc_start: 0.9332 (tpt) cc_final: 0.8686 (tpp) REVERT: D 355 ILE cc_start: 0.9649 (tp) cc_final: 0.9421 (tp) REVERT: D 454 CYS cc_start: 0.9336 (m) cc_final: 0.9043 (m) REVERT: D 485 MET cc_start: 0.9086 (mmp) cc_final: 0.7974 (mmm) REVERT: D 513 MET cc_start: 0.9284 (mmt) cc_final: 0.9001 (mmm) REVERT: D 644 MET cc_start: 0.9341 (mpp) cc_final: 0.8991 (mpp) REVERT: D 725 MET cc_start: 0.9386 (tpp) cc_final: 0.8692 (tpt) REVERT: D 743 MET cc_start: 0.7866 (tpt) cc_final: 0.7524 (tpp) REVERT: D 1143 ASP cc_start: 0.9227 (p0) cc_final: 0.8956 (t0) REVERT: D 1186 TYR cc_start: 0.8920 (m-10) cc_final: 0.8606 (m-10) REVERT: E 56 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9085 (tp30) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.3935 time to fit residues: 153.0602 Evaluate side-chains 181 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 288 optimal weight: 50.0000 chunk 236 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 375 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 344 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 278 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29868 Z= 0.181 Angle : 0.568 8.394 40748 Z= 0.302 Chirality : 0.043 0.160 4752 Planarity : 0.004 0.061 5163 Dihedral : 14.786 150.133 4863 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.28 (0.14), residues: 3767 helix: 0.27 (0.14), residues: 1330 sheet: -1.22 (0.24), residues: 452 loop : -1.55 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 686 HIS 0.004 0.001 HIS C 150 PHE 0.014 0.001 PHE C 57 TYR 0.014 0.001 TYR D 795 ARG 0.005 0.000 ARG D 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 3.369 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: A 142 MET cc_start: 0.9259 (pmm) cc_final: 0.8725 (pmm) REVERT: A 145 LYS cc_start: 0.9351 (tmtt) cc_final: 0.8847 (tptt) REVERT: C 85 CYS cc_start: 0.9464 (m) cc_final: 0.9234 (m) REVERT: C 403 MET cc_start: 0.9358 (tmm) cc_final: 0.9054 (tmm) REVERT: C 515 MET cc_start: 0.7670 (ptm) cc_final: 0.7059 (ptp) REVERT: C 516 ASP cc_start: 0.7814 (p0) cc_final: 0.7411 (p0) REVERT: C 549 ASP cc_start: 0.9376 (t0) cc_final: 0.9067 (t0) REVERT: C 653 MET cc_start: 0.8608 (tpt) cc_final: 0.8200 (tpt) REVERT: C 681 MET cc_start: 0.9476 (mmp) cc_final: 0.9220 (mmp) REVERT: C 685 MET cc_start: 0.9595 (mmp) cc_final: 0.9258 (mmm) REVERT: C 704 MET cc_start: 0.9424 (mmp) cc_final: 0.9187 (mmp) REVERT: C 794 LEU cc_start: 0.9642 (tt) cc_final: 0.9130 (pp) REVERT: C 805 MET cc_start: 0.8788 (ppp) cc_final: 0.8390 (ppp) REVERT: C 865 LEU cc_start: 0.9284 (mt) cc_final: 0.9023 (mt) REVERT: C 951 MET cc_start: 0.9228 (mmp) cc_final: 0.9024 (mmm) REVERT: C 1107 MET cc_start: 0.9326 (mpp) cc_final: 0.9114 (mpp) REVERT: C 1108 ASN cc_start: 0.9452 (m-40) cc_final: 0.8715 (t0) REVERT: C 1114 GLU cc_start: 0.9471 (tm-30) cc_final: 0.8519 (tm-30) REVERT: C 1230 MET cc_start: 0.8687 (tpt) cc_final: 0.7934 (tpp) REVERT: C 1232 MET cc_start: 0.9358 (mmp) cc_final: 0.9008 (mpp) REVERT: C 1273 MET cc_start: 0.9232 (mmp) cc_final: 0.8854 (mmp) REVERT: C 1329 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8803 (mt-10) REVERT: D 120 LEU cc_start: 0.9515 (mt) cc_final: 0.9073 (tp) REVERT: D 180 MET cc_start: 0.8354 (ppp) cc_final: 0.7890 (ppp) REVERT: D 245 LEU cc_start: 0.9344 (tp) cc_final: 0.9026 (tp) REVERT: D 265 LEU cc_start: 0.9850 (mp) cc_final: 0.9609 (pp) REVERT: D 329 ASP cc_start: 0.9109 (m-30) cc_final: 0.8837 (m-30) REVERT: D 330 MET cc_start: 0.9350 (tpt) cc_final: 0.8935 (tpp) REVERT: D 355 ILE cc_start: 0.9642 (tp) cc_final: 0.9436 (tp) REVERT: D 454 CYS cc_start: 0.9285 (m) cc_final: 0.9067 (m) REVERT: D 485 MET cc_start: 0.9136 (mmp) cc_final: 0.8106 (mmm) REVERT: D 513 MET cc_start: 0.9261 (mmt) cc_final: 0.8996 (mmm) REVERT: D 644 MET cc_start: 0.9335 (mpp) cc_final: 0.8941 (mpp) REVERT: D 725 MET cc_start: 0.9373 (tpp) cc_final: 0.8655 (tpt) REVERT: D 1143 ASP cc_start: 0.9204 (p0) cc_final: 0.8913 (t0) REVERT: D 1186 TYR cc_start: 0.8873 (m-10) cc_final: 0.8533 (m-10) REVERT: D 1254 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8997 (pt0) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3825 time to fit residues: 153.5741 Evaluate side-chains 187 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 233 optimal weight: 0.0000 chunk 348 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 330 optimal weight: 40.0000 chunk 99 optimal weight: 0.5980 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29868 Z= 0.172 Angle : 0.562 8.868 40748 Z= 0.297 Chirality : 0.042 0.150 4752 Planarity : 0.004 0.054 5163 Dihedral : 14.707 150.580 4863 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.14 (0.14), residues: 3767 helix: 0.45 (0.15), residues: 1319 sheet: -1.18 (0.24), residues: 455 loop : -1.50 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 686 HIS 0.003 0.001 HIS C 150 PHE 0.013 0.001 PHE C 186 TYR 0.016 0.001 TYR A 177 ARG 0.012 0.000 ARG D1048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 3.458 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: A 142 MET cc_start: 0.9272 (pmm) cc_final: 0.8686 (pmm) REVERT: A 145 LYS cc_start: 0.9371 (tmtt) cc_final: 0.8868 (tptt) REVERT: A 177 TYR cc_start: 0.6872 (m-80) cc_final: 0.6595 (m-80) REVERT: C 85 CYS cc_start: 0.9444 (m) cc_final: 0.9211 (m) REVERT: C 403 MET cc_start: 0.9369 (tmm) cc_final: 0.9062 (tmm) REVERT: C 515 MET cc_start: 0.7676 (ptm) cc_final: 0.7042 (ptp) REVERT: C 516 ASP cc_start: 0.7861 (p0) cc_final: 0.7438 (p0) REVERT: C 549 ASP cc_start: 0.9386 (t0) cc_final: 0.9068 (t0) REVERT: C 653 MET cc_start: 0.8578 (tpt) cc_final: 0.8224 (tpt) REVERT: C 681 MET cc_start: 0.9473 (mmp) cc_final: 0.9238 (mmp) REVERT: C 685 MET cc_start: 0.9602 (mmp) cc_final: 0.9290 (mmm) REVERT: C 704 MET cc_start: 0.9367 (mmp) cc_final: 0.9150 (mmp) REVERT: C 805 MET cc_start: 0.8829 (ppp) cc_final: 0.8469 (ppp) REVERT: C 865 LEU cc_start: 0.9254 (mt) cc_final: 0.8997 (mt) REVERT: C 951 MET cc_start: 0.9200 (mmp) cc_final: 0.8991 (mmm) REVERT: C 1107 MET cc_start: 0.9369 (mpp) cc_final: 0.9126 (mpp) REVERT: C 1108 ASN cc_start: 0.9452 (m-40) cc_final: 0.8684 (t0) REVERT: C 1114 GLU cc_start: 0.9477 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 1230 MET cc_start: 0.8879 (tpt) cc_final: 0.8373 (tpp) REVERT: C 1273 MET cc_start: 0.9219 (mmp) cc_final: 0.8904 (mmp) REVERT: C 1329 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8783 (mt-10) REVERT: D 120 LEU cc_start: 0.9541 (mt) cc_final: 0.9100 (tp) REVERT: D 180 MET cc_start: 0.8536 (ppp) cc_final: 0.7963 (ppp) REVERT: D 245 LEU cc_start: 0.9376 (tp) cc_final: 0.9053 (tp) REVERT: D 265 LEU cc_start: 0.9850 (mp) cc_final: 0.9602 (pp) REVERT: D 329 ASP cc_start: 0.9090 (m-30) cc_final: 0.8820 (m-30) REVERT: D 330 MET cc_start: 0.9389 (tpt) cc_final: 0.8925 (tpp) REVERT: D 454 CYS cc_start: 0.9238 (m) cc_final: 0.8916 (m) REVERT: D 484 MET cc_start: 0.8664 (mpp) cc_final: 0.8435 (mpp) REVERT: D 485 MET cc_start: 0.9133 (mmp) cc_final: 0.8040 (mmm) REVERT: D 644 MET cc_start: 0.9326 (mpp) cc_final: 0.8928 (mpp) REVERT: D 725 MET cc_start: 0.9328 (tpp) cc_final: 0.8500 (tpp) REVERT: D 743 MET cc_start: 0.8088 (tpt) cc_final: 0.7656 (tpp) REVERT: D 1040 MET cc_start: 0.8327 (ptp) cc_final: 0.8084 (mpp) REVERT: D 1143 ASP cc_start: 0.9211 (p0) cc_final: 0.8988 (t0) REVERT: D 1186 TYR cc_start: 0.8865 (m-10) cc_final: 0.8528 (m-10) REVERT: D 1254 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8942 (pt0) REVERT: E 18 ASP cc_start: 0.9510 (m-30) cc_final: 0.9268 (t0) outliers start: 3 outliers final: 1 residues processed: 231 average time/residue: 0.3745 time to fit residues: 147.2436 Evaluate side-chains 186 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 10.0000 chunk 209 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 274 optimal weight: 0.0370 chunk 152 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 255 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 overall best weight: 3.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29868 Z= 0.250 Angle : 0.597 9.871 40748 Z= 0.317 Chirality : 0.043 0.194 4752 Planarity : 0.004 0.051 5163 Dihedral : 14.704 151.802 4863 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.07 % Allowed : 3.84 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.12 (0.14), residues: 3767 helix: 0.48 (0.15), residues: 1319 sheet: -1.24 (0.24), residues: 467 loop : -1.48 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 686 HIS 0.005 0.001 HIS D 450 PHE 0.021 0.002 PHE D1145 TYR 0.018 0.001 TYR A 177 ARG 0.007 0.000 ARG D 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 3.454 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: A 142 MET cc_start: 0.9289 (pmm) cc_final: 0.8663 (pmm) REVERT: A 145 LYS cc_start: 0.9419 (tmtt) cc_final: 0.9043 (tptt) REVERT: A 177 TYR cc_start: 0.7248 (m-80) cc_final: 0.6872 (m-80) REVERT: C 85 CYS cc_start: 0.9477 (m) cc_final: 0.9245 (m) REVERT: C 403 MET cc_start: 0.9366 (tmm) cc_final: 0.9084 (tmm) REVERT: C 515 MET cc_start: 0.7810 (ptm) cc_final: 0.7205 (ptp) REVERT: C 516 ASP cc_start: 0.7845 (p0) cc_final: 0.7430 (p0) REVERT: C 549 ASP cc_start: 0.9416 (t0) cc_final: 0.9070 (t0) REVERT: C 653 MET cc_start: 0.8674 (tpt) cc_final: 0.8354 (tpt) REVERT: C 704 MET cc_start: 0.9384 (mmp) cc_final: 0.9178 (mmp) REVERT: C 805 MET cc_start: 0.8870 (ppp) cc_final: 0.8495 (ppp) REVERT: C 865 LEU cc_start: 0.9246 (mt) cc_final: 0.8960 (mt) REVERT: C 951 MET cc_start: 0.9194 (mmp) cc_final: 0.8974 (mmm) REVERT: C 1107 MET cc_start: 0.9367 (mpp) cc_final: 0.9101 (mpp) REVERT: C 1108 ASN cc_start: 0.9501 (m-40) cc_final: 0.8821 (t0) REVERT: C 1114 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9124 (tm-30) REVERT: C 1207 SER cc_start: 0.9425 (m) cc_final: 0.9198 (p) REVERT: C 1272 GLU cc_start: 0.8889 (pm20) cc_final: 0.8630 (pm20) REVERT: C 1329 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8823 (mt-10) REVERT: D 56 LEU cc_start: 0.9130 (tp) cc_final: 0.8704 (tt) REVERT: D 120 LEU cc_start: 0.9553 (mt) cc_final: 0.9084 (tp) REVERT: D 180 MET cc_start: 0.8685 (ppp) cc_final: 0.8133 (ppp) REVERT: D 245 LEU cc_start: 0.9359 (tp) cc_final: 0.9012 (tp) REVERT: D 265 LEU cc_start: 0.9851 (mp) cc_final: 0.9623 (pp) REVERT: D 329 ASP cc_start: 0.9068 (m-30) cc_final: 0.8849 (m-30) REVERT: D 330 MET cc_start: 0.9416 (tpt) cc_final: 0.8916 (tpp) REVERT: D 355 ILE cc_start: 0.9675 (tp) cc_final: 0.9445 (tp) REVERT: D 454 CYS cc_start: 0.9231 (m) cc_final: 0.8941 (m) REVERT: D 484 MET cc_start: 0.8847 (mpp) cc_final: 0.8596 (mpp) REVERT: D 485 MET cc_start: 0.9184 (mmp) cc_final: 0.7944 (mmm) REVERT: D 644 MET cc_start: 0.9284 (mpp) cc_final: 0.8861 (mpp) REVERT: D 725 MET cc_start: 0.9329 (tpp) cc_final: 0.8568 (tpp) REVERT: D 743 MET cc_start: 0.8099 (tpt) cc_final: 0.7801 (tpp) REVERT: D 1143 ASP cc_start: 0.9222 (p0) cc_final: 0.8788 (t0) REVERT: D 1186 TYR cc_start: 0.8867 (m-10) cc_final: 0.8501 (m-10) REVERT: D 1254 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8847 (mt-10) outliers start: 2 outliers final: 0 residues processed: 230 average time/residue: 0.3919 time to fit residues: 155.1173 Evaluate side-chains 186 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 7.9990 chunk 332 optimal weight: 40.0000 chunk 72 optimal weight: 10.0000 chunk 216 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 122 optimal weight: 0.0970 chunk 194 optimal weight: 0.0670 overall best weight: 2.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29868 Z= 0.175 Angle : 0.566 9.930 40748 Z= 0.296 Chirality : 0.043 0.160 4752 Planarity : 0.004 0.065 5163 Dihedral : 14.650 151.090 4863 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -0.98 (0.14), residues: 3767 helix: 0.61 (0.15), residues: 1315 sheet: -1.10 (0.24), residues: 438 loop : -1.43 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 686 HIS 0.003 0.001 HIS C 150 PHE 0.022 0.001 PHE C 186 TYR 0.015 0.001 TYR D 631 ARG 0.006 0.000 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 3.553 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: A 142 MET cc_start: 0.9321 (pmm) cc_final: 0.8650 (pmm) REVERT: A 145 LYS cc_start: 0.9415 (tmtt) cc_final: 0.9041 (tptt) REVERT: A 158 ARG cc_start: 0.8766 (mpt90) cc_final: 0.8537 (mpt180) REVERT: A 177 TYR cc_start: 0.7251 (m-80) cc_final: 0.6780 (m-80) REVERT: B 35 PHE cc_start: 0.9173 (m-80) cc_final: 0.8940 (m-10) REVERT: C 85 CYS cc_start: 0.9452 (m) cc_final: 0.9224 (m) REVERT: C 403 MET cc_start: 0.9399 (tmm) cc_final: 0.9088 (tmm) REVERT: C 515 MET cc_start: 0.7808 (ptm) cc_final: 0.7176 (ptp) REVERT: C 516 ASP cc_start: 0.7790 (p0) cc_final: 0.7357 (p0) REVERT: C 549 ASP cc_start: 0.9396 (t0) cc_final: 0.9099 (t0) REVERT: C 653 MET cc_start: 0.8643 (tpt) cc_final: 0.8408 (tpt) REVERT: C 681 MET cc_start: 0.9455 (mmp) cc_final: 0.9247 (mmp) REVERT: C 805 MET cc_start: 0.8908 (ppp) cc_final: 0.8516 (ppp) REVERT: C 865 LEU cc_start: 0.9224 (mt) cc_final: 0.8941 (mt) REVERT: C 1107 MET cc_start: 0.9388 (mpp) cc_final: 0.9104 (mpp) REVERT: C 1108 ASN cc_start: 0.9445 (m-40) cc_final: 0.8591 (t0) REVERT: C 1114 GLU cc_start: 0.9444 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 1230 MET cc_start: 0.8840 (tpt) cc_final: 0.8000 (tpp) REVERT: C 1273 MET cc_start: 0.9272 (mmp) cc_final: 0.8422 (tpt) REVERT: C 1279 GLU cc_start: 0.9546 (tp30) cc_final: 0.9337 (tp30) REVERT: C 1329 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8794 (mt-10) REVERT: D 120 LEU cc_start: 0.9544 (mt) cc_final: 0.9066 (tp) REVERT: D 180 MET cc_start: 0.8683 (ppp) cc_final: 0.8445 (ppp) REVERT: D 245 LEU cc_start: 0.9396 (tp) cc_final: 0.9035 (tp) REVERT: D 265 LEU cc_start: 0.9846 (mp) cc_final: 0.9614 (pp) REVERT: D 329 ASP cc_start: 0.9108 (m-30) cc_final: 0.8859 (m-30) REVERT: D 330 MET cc_start: 0.9387 (tpt) cc_final: 0.8855 (tpp) REVERT: D 355 ILE cc_start: 0.9654 (tp) cc_final: 0.9436 (tp) REVERT: D 454 CYS cc_start: 0.9197 (m) cc_final: 0.8977 (m) REVERT: D 478 LEU cc_start: 0.9789 (mm) cc_final: 0.9527 (mt) REVERT: D 485 MET cc_start: 0.9178 (mmp) cc_final: 0.8128 (mmm) REVERT: D 644 MET cc_start: 0.9284 (mpp) cc_final: 0.8863 (mpp) REVERT: D 720 ASN cc_start: 0.9234 (t0) cc_final: 0.8741 (t0) REVERT: D 725 MET cc_start: 0.9356 (tpp) cc_final: 0.8582 (tpp) REVERT: D 743 MET cc_start: 0.8055 (tpt) cc_final: 0.7796 (tpp) REVERT: D 1143 ASP cc_start: 0.9191 (p0) cc_final: 0.8745 (t0) REVERT: D 1186 TYR cc_start: 0.8778 (m-10) cc_final: 0.8401 (m-10) REVERT: E 18 ASP cc_start: 0.9497 (m-30) cc_final: 0.9264 (t0) REVERT: E 26 ARG cc_start: 0.9505 (tpm170) cc_final: 0.9118 (tpt170) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3857 time to fit residues: 152.3946 Evaluate side-chains 191 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 8.9990 chunk 41 optimal weight: 0.0980 chunk 210 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 209 optimal weight: 40.0000 chunk 311 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 368 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 700 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29868 Z= 0.183 Angle : 0.573 9.520 40748 Z= 0.301 Chirality : 0.043 0.180 4752 Planarity : 0.004 0.054 5163 Dihedral : 14.624 150.971 4863 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.58 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -0.94 (0.14), residues: 3767 helix: 0.65 (0.15), residues: 1318 sheet: -1.05 (0.25), residues: 435 loop : -1.40 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 686 HIS 0.004 0.001 HIS C1313 PHE 0.026 0.001 PHE D 227 TYR 0.014 0.001 TYR A 177 ARG 0.005 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 3.497 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: A 142 MET cc_start: 0.9204 (pmm) cc_final: 0.8566 (pmm) REVERT: A 145 LYS cc_start: 0.9419 (tmtt) cc_final: 0.9047 (tptt) REVERT: A 158 ARG cc_start: 0.8788 (mpt90) cc_final: 0.8557 (mpt180) REVERT: A 177 TYR cc_start: 0.7329 (m-80) cc_final: 0.6775 (m-80) REVERT: C 85 CYS cc_start: 0.9445 (m) cc_final: 0.9217 (m) REVERT: C 403 MET cc_start: 0.9379 (tmm) cc_final: 0.9086 (tmm) REVERT: C 515 MET cc_start: 0.7824 (ptm) cc_final: 0.7173 (ptp) REVERT: C 516 ASP cc_start: 0.7701 (p0) cc_final: 0.7266 (p0) REVERT: C 549 ASP cc_start: 0.9385 (t0) cc_final: 0.9066 (t0) REVERT: C 653 MET cc_start: 0.8711 (tpt) cc_final: 0.8365 (tpt) REVERT: C 805 MET cc_start: 0.8967 (ppp) cc_final: 0.8591 (ppp) REVERT: C 865 LEU cc_start: 0.9236 (mt) cc_final: 0.8938 (mt) REVERT: C 951 MET cc_start: 0.9153 (mmp) cc_final: 0.8864 (mmm) REVERT: C 1107 MET cc_start: 0.9395 (mpp) cc_final: 0.9099 (mpp) REVERT: C 1108 ASN cc_start: 0.9464 (m-40) cc_final: 0.8593 (t0) REVERT: C 1114 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9062 (tm-30) REVERT: C 1207 SER cc_start: 0.9430 (m) cc_final: 0.9201 (p) REVERT: C 1272 GLU cc_start: 0.8084 (pp20) cc_final: 0.7835 (pm20) REVERT: C 1279 GLU cc_start: 0.9546 (tp30) cc_final: 0.9324 (tp30) REVERT: C 1290 MET cc_start: 0.9196 (ttt) cc_final: 0.8996 (ppp) REVERT: C 1329 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8738 (mt-10) REVERT: D 120 LEU cc_start: 0.9545 (mt) cc_final: 0.9044 (tp) REVERT: D 180 MET cc_start: 0.8442 (ppp) cc_final: 0.7828 (ppp) REVERT: D 245 LEU cc_start: 0.9399 (tp) cc_final: 0.9065 (tp) REVERT: D 265 LEU cc_start: 0.9848 (mp) cc_final: 0.9620 (pp) REVERT: D 329 ASP cc_start: 0.9106 (m-30) cc_final: 0.8850 (m-30) REVERT: D 330 MET cc_start: 0.9332 (tpt) cc_final: 0.8826 (tpt) REVERT: D 355 ILE cc_start: 0.9637 (tp) cc_final: 0.9420 (tp) REVERT: D 454 CYS cc_start: 0.9206 (m) cc_final: 0.8987 (m) REVERT: D 484 MET cc_start: 0.8659 (mpp) cc_final: 0.8454 (mpp) REVERT: D 485 MET cc_start: 0.9161 (mmp) cc_final: 0.8019 (mmm) REVERT: D 644 MET cc_start: 0.9243 (mpp) cc_final: 0.8830 (mpp) REVERT: D 720 ASN cc_start: 0.9206 (t0) cc_final: 0.8744 (t0) REVERT: D 725 MET cc_start: 0.9340 (tpp) cc_final: 0.8442 (tpp) REVERT: D 1040 MET cc_start: 0.8386 (ptp) cc_final: 0.8141 (mpp) REVERT: D 1143 ASP cc_start: 0.9202 (p0) cc_final: 0.8809 (t0) REVERT: E 18 ASP cc_start: 0.9495 (m-30) cc_final: 0.9259 (t0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3894 time to fit residues: 150.5755 Evaluate side-chains 185 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 219 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 182 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29868 Z= 0.259 Angle : 0.610 9.061 40748 Z= 0.322 Chirality : 0.043 0.198 4752 Planarity : 0.004 0.057 5163 Dihedral : 14.646 151.365 4863 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.05 (0.14), residues: 3767 helix: 0.58 (0.15), residues: 1315 sheet: -1.24 (0.24), residues: 448 loop : -1.45 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C1276 HIS 0.005 0.001 HIS D 450 PHE 0.017 0.002 PHE D1145 TYR 0.017 0.001 TYR D 457 ARG 0.004 0.000 ARG D1148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.499 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: A 142 MET cc_start: 0.9205 (pmm) cc_final: 0.8600 (pmm) REVERT: A 145 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9063 (tptt) REVERT: A 158 ARG cc_start: 0.8806 (mpt90) cc_final: 0.8573 (mpt180) REVERT: A 177 TYR cc_start: 0.7620 (m-80) cc_final: 0.7083 (m-80) REVERT: C 85 CYS cc_start: 0.9470 (m) cc_final: 0.9244 (m) REVERT: C 403 MET cc_start: 0.9403 (tmm) cc_final: 0.9120 (tmm) REVERT: C 515 MET cc_start: 0.7922 (ptm) cc_final: 0.7290 (ptp) REVERT: C 516 ASP cc_start: 0.7579 (p0) cc_final: 0.7201 (p0) REVERT: C 549 ASP cc_start: 0.9431 (t0) cc_final: 0.9113 (t0) REVERT: C 653 MET cc_start: 0.8738 (tpt) cc_final: 0.8390 (tpt) REVERT: C 681 MET cc_start: 0.9508 (mmp) cc_final: 0.9286 (mmp) REVERT: C 805 MET cc_start: 0.8911 (ppp) cc_final: 0.8446 (ppp) REVERT: C 865 LEU cc_start: 0.9237 (mt) cc_final: 0.8920 (mt) REVERT: C 883 LEU cc_start: 0.8809 (mp) cc_final: 0.8608 (mp) REVERT: C 951 MET cc_start: 0.9180 (mmp) cc_final: 0.8964 (mmm) REVERT: C 1107 MET cc_start: 0.9382 (mpp) cc_final: 0.9105 (mpp) REVERT: C 1108 ASN cc_start: 0.9517 (m-40) cc_final: 0.8732 (t0) REVERT: C 1114 GLU cc_start: 0.9455 (tm-30) cc_final: 0.8947 (tm-30) REVERT: C 1207 SER cc_start: 0.9443 (m) cc_final: 0.9229 (p) REVERT: C 1232 MET cc_start: 0.9322 (mmp) cc_final: 0.9101 (mmp) REVERT: C 1329 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8802 (mt-10) REVERT: D 56 LEU cc_start: 0.9115 (tp) cc_final: 0.8830 (tp) REVERT: D 120 LEU cc_start: 0.9567 (mt) cc_final: 0.9037 (tp) REVERT: D 180 MET cc_start: 0.8610 (ppp) cc_final: 0.8246 (ppp) REVERT: D 245 LEU cc_start: 0.9392 (tp) cc_final: 0.9051 (tp) REVERT: D 265 LEU cc_start: 0.9851 (mp) cc_final: 0.9650 (pp) REVERT: D 329 ASP cc_start: 0.9073 (m-30) cc_final: 0.8868 (m-30) REVERT: D 330 MET cc_start: 0.9388 (tpt) cc_final: 0.8908 (tpt) REVERT: D 355 ILE cc_start: 0.9643 (tp) cc_final: 0.9435 (tp) REVERT: D 454 CYS cc_start: 0.9170 (m) cc_final: 0.8848 (m) REVERT: D 485 MET cc_start: 0.9202 (mmp) cc_final: 0.8108 (mmm) REVERT: D 644 MET cc_start: 0.9240 (mpp) cc_final: 0.8833 (mpp) REVERT: D 725 MET cc_start: 0.9346 (tpp) cc_final: 0.8447 (tpp) REVERT: D 743 MET cc_start: 0.8219 (tpt) cc_final: 0.7759 (tpp) REVERT: D 1040 MET cc_start: 0.8430 (ptp) cc_final: 0.8137 (mpp) REVERT: D 1143 ASP cc_start: 0.9225 (p0) cc_final: 0.8828 (t0) REVERT: D 1186 TYR cc_start: 0.8769 (m-10) cc_final: 0.8482 (m-10) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3939 time to fit residues: 145.4981 Evaluate side-chains 180 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 5.9990 chunk 352 optimal weight: 0.9990 chunk 321 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 206 optimal weight: 0.8980 chunk 149 optimal weight: 40.0000 chunk 269 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 324 optimal weight: 10.0000 chunk 341 optimal weight: 40.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29868 Z= 0.282 Angle : 0.634 10.407 40748 Z= 0.335 Chirality : 0.044 0.206 4752 Planarity : 0.004 0.055 5163 Dihedral : 14.677 151.616 4863 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.11 (0.14), residues: 3767 helix: 0.57 (0.15), residues: 1300 sheet: -1.32 (0.24), residues: 468 loop : -1.50 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C1276 HIS 0.005 0.001 HIS C 150 PHE 0.017 0.002 PHE C 506 TYR 0.017 0.002 TYR D 631 ARG 0.015 0.001 ARG D 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.731 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: A 142 MET cc_start: 0.9211 (pmm) cc_final: 0.8610 (pmm) REVERT: A 145 LYS cc_start: 0.9447 (tmtt) cc_final: 0.9064 (tptt) REVERT: A 177 TYR cc_start: 0.7793 (m-80) cc_final: 0.7194 (m-80) REVERT: C 85 CYS cc_start: 0.9492 (m) cc_final: 0.9261 (m) REVERT: C 403 MET cc_start: 0.9426 (tmm) cc_final: 0.9134 (tmm) REVERT: C 515 MET cc_start: 0.7962 (ptm) cc_final: 0.7310 (ptp) REVERT: C 516 ASP cc_start: 0.7496 (p0) cc_final: 0.7159 (p0) REVERT: C 549 ASP cc_start: 0.9436 (t0) cc_final: 0.9127 (t0) REVERT: C 653 MET cc_start: 0.8808 (tpt) cc_final: 0.8389 (tpt) REVERT: C 681 MET cc_start: 0.9513 (mmp) cc_final: 0.9310 (mmp) REVERT: C 704 MET cc_start: 0.9377 (mmp) cc_final: 0.9137 (mmp) REVERT: C 805 MET cc_start: 0.8977 (ppp) cc_final: 0.8587 (ppp) REVERT: C 951 MET cc_start: 0.9166 (mmp) cc_final: 0.8946 (mmm) REVERT: C 1107 MET cc_start: 0.9349 (mpp) cc_final: 0.9081 (mpp) REVERT: C 1108 ASN cc_start: 0.9520 (m-40) cc_final: 0.8799 (t0) REVERT: C 1114 GLU cc_start: 0.9476 (tm-30) cc_final: 0.9020 (tm-30) REVERT: C 1207 SER cc_start: 0.9454 (m) cc_final: 0.9243 (p) REVERT: C 1329 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8817 (mt-10) REVERT: D 56 LEU cc_start: 0.9045 (tp) cc_final: 0.8675 (tp) REVERT: D 120 LEU cc_start: 0.9601 (mt) cc_final: 0.9059 (tp) REVERT: D 180 MET cc_start: 0.8651 (ppp) cc_final: 0.8317 (ppp) REVERT: D 245 LEU cc_start: 0.9420 (tp) cc_final: 0.9098 (tp) REVERT: D 330 MET cc_start: 0.9437 (tpt) cc_final: 0.8933 (tpt) REVERT: D 355 ILE cc_start: 0.9645 (tp) cc_final: 0.9436 (tp) REVERT: D 454 CYS cc_start: 0.9149 (m) cc_final: 0.8856 (m) REVERT: D 484 MET cc_start: 0.8832 (mpp) cc_final: 0.8454 (mpp) REVERT: D 485 MET cc_start: 0.9214 (mmp) cc_final: 0.8146 (mmm) REVERT: D 644 MET cc_start: 0.9237 (mpp) cc_final: 0.8827 (mpp) REVERT: D 725 MET cc_start: 0.9337 (tpp) cc_final: 0.8459 (tpp) REVERT: D 743 MET cc_start: 0.8339 (tpt) cc_final: 0.7958 (tpp) REVERT: D 1040 MET cc_start: 0.8398 (ptp) cc_final: 0.8124 (mpp) REVERT: D 1143 ASP cc_start: 0.9251 (p0) cc_final: 0.8786 (t0) REVERT: D 1186 TYR cc_start: 0.8851 (m-10) cc_final: 0.8564 (m-10) REVERT: E 18 ASP cc_start: 0.9517 (m-30) cc_final: 0.9285 (t0) REVERT: E 26 ARG cc_start: 0.9527 (tpm170) cc_final: 0.9080 (tpm170) REVERT: E 30 MET cc_start: 0.8689 (mpp) cc_final: 0.8222 (mpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3924 time to fit residues: 142.3399 Evaluate side-chains 176 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 6.9990 chunk 362 optimal weight: 20.0000 chunk 221 optimal weight: 0.7980 chunk 172 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 380 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 234 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 overall best weight: 3.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29868 Z= 0.256 Angle : 0.618 10.352 40748 Z= 0.326 Chirality : 0.044 0.227 4752 Planarity : 0.004 0.053 5163 Dihedral : 14.659 151.565 4863 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.35 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.10 (0.14), residues: 3767 helix: 0.53 (0.15), residues: 1309 sheet: -1.26 (0.24), residues: 468 loop : -1.48 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C1276 HIS 0.005 0.001 HIS C 150 PHE 0.016 0.002 PHE D 461 TYR 0.014 0.001 TYR A 177 ARG 0.007 0.000 ARG D 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.473 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: A 142 MET cc_start: 0.9203 (pmm) cc_final: 0.8541 (pmm) REVERT: A 145 LYS cc_start: 0.9452 (tmtt) cc_final: 0.9105 (tptt) REVERT: A 177 TYR cc_start: 0.7738 (m-80) cc_final: 0.7131 (m-80) REVERT: B 51 MET cc_start: 0.9233 (tpt) cc_final: 0.8983 (tpp) REVERT: C 85 CYS cc_start: 0.9486 (m) cc_final: 0.9256 (m) REVERT: C 403 MET cc_start: 0.9431 (tmm) cc_final: 0.9134 (tmm) REVERT: C 515 MET cc_start: 0.7960 (ptm) cc_final: 0.7391 (ptm) REVERT: C 516 ASP cc_start: 0.7439 (p0) cc_final: 0.7089 (p0) REVERT: C 549 ASP cc_start: 0.9437 (t0) cc_final: 0.9133 (t0) REVERT: C 653 MET cc_start: 0.8816 (tpt) cc_final: 0.8439 (tpt) REVERT: C 681 MET cc_start: 0.9513 (mmp) cc_final: 0.9310 (mmp) REVERT: C 704 MET cc_start: 0.9360 (mmp) cc_final: 0.9105 (mmp) REVERT: C 805 MET cc_start: 0.8980 (ppp) cc_final: 0.8588 (ppp) REVERT: C 951 MET cc_start: 0.9164 (mmp) cc_final: 0.8954 (mmm) REVERT: C 1107 MET cc_start: 0.9345 (mpp) cc_final: 0.9074 (mpp) REVERT: C 1108 ASN cc_start: 0.9515 (m-40) cc_final: 0.8743 (t0) REVERT: C 1114 GLU cc_start: 0.9431 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 1207 SER cc_start: 0.9462 (m) cc_final: 0.9251 (p) REVERT: C 1230 MET cc_start: 0.8726 (tpt) cc_final: 0.8076 (tpp) REVERT: C 1279 GLU cc_start: 0.9578 (tp30) cc_final: 0.9363 (tp30) REVERT: C 1290 MET cc_start: 0.8941 (ppp) cc_final: 0.8514 (ppp) REVERT: C 1329 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8790 (mt-10) REVERT: D 56 LEU cc_start: 0.9051 (tp) cc_final: 0.8693 (tp) REVERT: D 120 LEU cc_start: 0.9592 (mt) cc_final: 0.9058 (tp) REVERT: D 180 MET cc_start: 0.8650 (ppp) cc_final: 0.8334 (ppp) REVERT: D 245 LEU cc_start: 0.9408 (tp) cc_final: 0.9089 (tp) REVERT: D 329 ASP cc_start: 0.9116 (m-30) cc_final: 0.8864 (m-30) REVERT: D 330 MET cc_start: 0.9443 (tpt) cc_final: 0.8925 (tpt) REVERT: D 355 ILE cc_start: 0.9645 (tp) cc_final: 0.9436 (tp) REVERT: D 443 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8775 (tm-30) REVERT: D 454 CYS cc_start: 0.9143 (m) cc_final: 0.8859 (m) REVERT: D 479 GLU cc_start: 0.8847 (pt0) cc_final: 0.8613 (pt0) REVERT: D 484 MET cc_start: 0.8842 (mpp) cc_final: 0.8516 (mpp) REVERT: D 485 MET cc_start: 0.9226 (mmp) cc_final: 0.8188 (mmm) REVERT: D 644 MET cc_start: 0.9244 (mpp) cc_final: 0.8842 (mpp) REVERT: D 725 MET cc_start: 0.9333 (tpp) cc_final: 0.8459 (tpp) REVERT: D 743 MET cc_start: 0.8293 (tpt) cc_final: 0.7892 (tpp) REVERT: D 1040 MET cc_start: 0.8480 (ptp) cc_final: 0.8175 (mpp) REVERT: D 1143 ASP cc_start: 0.9230 (p0) cc_final: 0.8742 (t0) REVERT: D 1186 TYR cc_start: 0.8802 (m-10) cc_final: 0.8497 (m-10) REVERT: E 26 ARG cc_start: 0.9527 (tpm170) cc_final: 0.9091 (tpm170) REVERT: E 30 MET cc_start: 0.8693 (mpp) cc_final: 0.8297 (mpp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3908 time to fit residues: 141.8642 Evaluate side-chains 174 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 chunk 84 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.054187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034612 restraints weight = 207245.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035808 restraints weight = 115711.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036610 restraints weight = 77596.473| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29868 Z= 0.301 Angle : 0.651 10.241 40748 Z= 0.343 Chirality : 0.044 0.203 4752 Planarity : 0.004 0.054 5163 Dihedral : 14.671 151.748 4863 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.04 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % 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: -1.20 (0.14), residues: 3767 helix: 0.44 (0.15), residues: 1303 sheet: -1.27 (0.23), residues: 482 loop : -1.54 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP C1276 HIS 0.006 0.001 HIS C 150 PHE 0.017 0.002 PHE D 461 TYR 0.016 0.002 TYR A 68 ARG 0.008 0.001 ARG D 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4961.73 seconds wall clock time: 92 minutes 35.43 seconds (5555.43 seconds total)