Starting phenix.real_space_refine on Tue Jul 23 05:38:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoq_14848/07_2024/7zoq_14848_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoq_14848/07_2024/7zoq_14848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoq_14848/07_2024/7zoq_14848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoq_14848/07_2024/7zoq_14848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoq_14848/07_2024/7zoq_14848_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoq_14848/07_2024/7zoq_14848_neut.cif" } resolution = 3.2 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= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 38 5.49 5 S 73 5.16 5 C 13121 2.51 5 N 3653 2.21 5 O 3977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B ASP 682": "OD1" <-> "OD2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1277": "OD1" <-> "OD2" Residue "B GLU 1416": "OE1" <-> "OE2" Residue "B PHE 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1466": "OE1" <-> "OE2" Residue "B GLU 1754": "OE1" <-> "OE2" Residue "B GLU 1775": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20866 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6637 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 28, 'TRANS': 783} Chain breaks: 1 Chain: "B" Number of atoms: 13412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1702, 13403 Classifications: {'peptide': 1702} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 84, 'TRANS': 1617} Chain breaks: 7 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 259 Conformer: "B" Number of residues, atoms: 1702, 13403 Classifications: {'peptide': 1702} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 84, 'TRANS': 1617} Chain breaks: 7 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 259 bond proxies already assigned to first conformer: 13670 Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 813 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 3, 'rna3p_pyr': 12} Link IDs: {'rna2p': 22, 'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14061 SG CYS B 997 45.028 71.327 125.559 1.00 24.19 S ATOM 17761 SG CYS B1515 43.831 70.092 122.214 1.00 23.98 S ATOM 18010 SG CYS B1545 42.632 73.448 123.760 1.00 20.16 S ATOM 18028 SG CYS B1548 46.094 73.164 122.336 1.00 18.28 S ATOM 7316 SG CYS B 97 92.075 75.162 39.769 1.00 41.05 S ATOM 7591 SG CYS B 131 95.146 73.201 38.468 1.00 63.59 S ATOM 7641 SG CYS B 137 95.354 75.246 41.719 1.00 42.75 S ATOM 7665 SG CYS B 140 93.216 72.148 41.559 1.00 37.66 S ATOM 10363 SG CYS B 498 65.453 80.350 63.928 1.00 34.05 S ATOM 10440 SG CYS B 508 66.298 79.054 60.534 1.00 41.08 S ATOM 10452 SG CYS B 510 66.669 82.823 61.196 1.00 30.22 S ATOM 10472 SG CYS B 513 69.050 80.320 62.816 1.00 28.09 S ATOM 12156 SG CYS B 757 43.748 79.067 87.105 1.00 51.71 S ATOM 12168 SG CYS B 759 45.021 82.313 88.698 1.00 36.29 S ATOM 12189 SG CYS B 762 47.548 79.648 87.573 1.00 31.88 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B1526 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B1526 " occ=0.50 Time building chain proxies: 18.65, per 1000 atoms: 0.89 Number of scatterers: 20866 At special positions: 0 Unit cell: (122.582, 123.859, 219.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 73 16.00 P 38 15.00 O 3977 8.00 N 3653 7.00 C 13121 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: 7.74 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 997 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1545 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1548 " pdb="ZN ZN B1801 " - pdb=" SG CYS B1515 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 140 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 97 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 137 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 131 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 508 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 513 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 510 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" ND1 HIS B 754 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 759 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 757 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 762 " Number of angles added : 21 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 26 sheets defined 40.9% alpha, 10.5% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 6.81 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 60 through 79 Processing helix chain 'A' and resid 83 through 118 removed outlier: 4.001A pdb=" N ASN A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 149 removed outlier: 4.104A pdb=" N LYS A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 removed outlier: 3.731A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 224 through 245 removed outlier: 3.772A pdb=" N LYS A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 removed outlier: 4.482A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 5.783A pdb=" N PHE A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.817A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 removed outlier: 4.197A pdb=" N GLU A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 4.571A pdb=" N VAL A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 Processing helix chain 'A' and resid 400 through 418 removed outlier: 4.248A pdb=" N ALA A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.581A pdb=" N GLU A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 533 Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.940A pdb=" N LYS A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU A 539 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 540 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 557 through 560 Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.902A pdb=" N ASN A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.849A pdb=" N HIS A 591 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.873A pdb=" N LYS A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 removed outlier: 4.189A pdb=" N SER A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.511A pdb=" N ILE A 658 " --> pdb=" O LYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 removed outlier: 3.516A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 698 Processing helix chain 'A' and resid 707 through 713 removed outlier: 4.218A pdb=" N LEU A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 745 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 766 through 780 removed outlier: 3.695A pdb=" N VAL A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 791 removed outlier: 3.549A pdb=" N LYS A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 800 through 808 removed outlier: 3.675A pdb=" N LEU A 804 " --> pdb=" O GLN A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.569A pdb=" N ARG B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 68 through 87 removed outlier: 4.081A pdb=" N VAL B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 145 through 148 removed outlier: 3.524A pdb=" N LYS B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 148' Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 291 through 310 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 314 through 329 removed outlier: 4.004A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 removed outlier: 3.874A pdb=" N PHE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 401 Processing helix chain 'B' and resid 478 through 495 removed outlier: 3.534A pdb=" N LEU B 482 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.947A pdb=" N CYS B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.553A pdb=" N GLN B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.682A pdb=" N THR B 602 " --> pdb=" O ASP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 630 removed outlier: 3.924A pdb=" N THR B 629 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.595A pdb=" N LEU B 675 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 748 removed outlier: 3.522A pdb=" N PHE B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 858 through 862 removed outlier: 3.794A pdb=" N GLY B 862 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.686A pdb=" N LYS B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 995 removed outlier: 4.162A pdb=" N ILE B 982 " --> pdb=" O PRO B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1065 removed outlier: 3.525A pdb=" N ASN B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 4.194A pdb=" N LEU B1079 " --> pdb=" O THR B1075 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B1080 " --> pdb=" O ASP B1076 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1084 " --> pdb=" O GLU B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1101 Proline residue: B1097 - end of helix Processing helix chain 'B' and resid 1107 through 1120 removed outlier: 3.725A pdb=" N ASP B1114 " --> pdb=" O THR B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1124 Processing helix chain 'B' and resid 1125 through 1133 Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.807A pdb=" N LEU B1145 " --> pdb=" O THR B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1165 removed outlier: 4.025A pdb=" N LEU B1165 " --> pdb=" O GLN B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1184 removed outlier: 3.560A pdb=" N VAL B1184 " --> pdb=" O LEU B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1196 removed outlier: 3.545A pdb=" N LEU B1196 " --> pdb=" O ILE B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1199 No H-bonds generated for 'chain 'B' and resid 1197 through 1199' Processing helix chain 'B' and resid 1206 through 1216 Processing helix chain 'B' and resid 1219 through 1229 removed outlier: 3.930A pdb=" N VAL B1223 " --> pdb=" O PRO B1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1259 removed outlier: 3.885A pdb=" N HIS B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1274 through 1283 Processing helix chain 'B' and resid 1431 through 1452 removed outlier: 3.925A pdb=" N GLU B1435 " --> pdb=" O PRO B1431 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B1445 " --> pdb=" O THR B1441 " (cutoff:3.500A) Processing helix chain 'B' and resid 1500 through 1504 removed outlier: 3.548A pdb=" N ARG B1503 " --> pdb=" O VAL B1500 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1523 removed outlier: 3.920A pdb=" N ASP B1521 " --> pdb=" O GLU B1518 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B1522 " --> pdb=" O ILE B1519 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU B1523 " --> pdb=" O LEU B1520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1518 through 1523' Processing helix chain 'B' and resid 1524 through 1532 Processing helix chain 'B' and resid 1545 through 1552 Processing helix chain 'B' and resid 1574 through 1579 removed outlier: 3.890A pdb=" N ASN B1577 " --> pdb=" O LEU B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1613 through 1621 removed outlier: 3.568A pdb=" N VAL B1617 " --> pdb=" O GLY B1613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1671 Processing helix chain 'B' and resid 1683 through 1687 Processing helix chain 'B' and resid 1706 through 1723 removed outlier: 3.572A pdb=" N LEU B1710 " --> pdb=" O ASP B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1736 removed outlier: 3.502A pdb=" N LEU B1736 " --> pdb=" O LEU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1763 through 1768 Processing helix chain 'B' and resid 1772 through 1777 removed outlier: 3.840A pdb=" N GLN B1776 " --> pdb=" O TYR B1772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.741A pdb=" N ASN A 496 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 489 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 482 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE A 585 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 484 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 663 through 664 removed outlier: 3.536A pdb=" N GLU A 639 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR A 761 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 758 " --> pdb=" O TYR A 813 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.464A pdb=" N HIS A 687 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.561A pdb=" N TYR B 254 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.512A pdb=" N ARG B 185 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.528A pdb=" N ARG B 53 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 66 " --> pdb=" O ARG B 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.851A pdb=" N TYR B 91 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 188 through 190 removed outlier: 6.767A pdb=" N ARG B 189 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 519 through 521 removed outlier: 3.530A pdb=" N GLY B 441 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 613 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 442 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN B 611 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 444 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 609 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.953A pdb=" N LYS B 466 " --> pdb=" O TRP B 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 476 through 477 removed outlier: 3.648A pdb=" N SER B 524 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 534 through 538 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.783A pdb=" N THR B 547 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 653 through 662 removed outlier: 4.759A pdb=" N LYS B 822 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR B 728 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 727 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 653 through 662 Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'B' and resid 902 through 904 removed outlier: 4.208A pdb=" N GLY B1789 " --> pdb=" O ILE B 903 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 907 through 910 Processing sheet with id=AC2, first strand: chain 'B' and resid 1560 through 1562 removed outlier: 3.518A pdb=" N PHE B1651 " --> pdb=" O CYS B 943 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR B 937 " --> pdb=" O ASN B1657 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 940 " --> pdb=" O ILE B1698 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE B1698 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 942 " --> pdb=" O GLY B1696 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.826A pdb=" N GLU B 957 " --> pdb=" O ASP B 967 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP B 967 " --> pdb=" O GLU B 957 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 965 " --> pdb=" O GLN B 959 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1044 through 1047 Processing sheet with id=AC5, first strand: chain 'B' and resid 1169 through 1170 removed outlier: 3.517A pdb=" N VAL B1138 " --> pdb=" O TYR B1170 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG B1135 " --> pdb=" O ARG B1204 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B1204 " --> pdb=" O ARG B1135 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS B1137 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B1139 " --> pdb=" O ASP B1200 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP B1200 " --> pdb=" O ARG B1139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1378 through 1379 removed outlier: 3.780A pdb=" N ARG B1391 " --> pdb=" O ILE B1379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1474 through 1477 removed outlier: 4.039A pdb=" N ARG B1476 " --> pdb=" O ASP B1486 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP B1486 " --> pdb=" O ARG B1476 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1581 through 1583 removed outlier: 4.349A pdb=" N ARG B1638 " --> pdb=" O LEU B1583 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 8.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3731 1.32 - 1.45: 5496 1.45 - 1.57: 11966 1.57 - 1.70: 76 1.70 - 1.82: 108 Bond restraints: 21377 Sorted by residual: bond pdb=" C BLYS B1526 " pdb=" N GLU B1527 " ideal model delta sigma weight residual 1.334 1.418 -0.084 1.33e-02 5.65e+03 4.00e+01 bond pdb=" C GLN B1525 " pdb=" N BLYS B1526 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.31e-02 5.83e+03 2.52e+01 bond pdb=" N ARG B 409 " pdb=" CA ARG B 409 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N ASP B 310 " pdb=" CA ASP B 310 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" C ALA B 305 " pdb=" O ALA B 305 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.17e-02 7.31e+03 1.04e+01 ... (remaining 21372 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.47: 759 106.47 - 113.40: 11475 113.40 - 120.33: 7856 120.33 - 127.27: 8615 127.27 - 134.20: 290 Bond angle restraints: 28995 Sorted by residual: angle pdb=" N PRO B 277 " pdb=" CA PRO B 277 " pdb=" CB PRO B 277 " ideal model delta sigma weight residual 101.83 110.02 -8.19 8.40e-01 1.42e+00 9.51e+01 angle pdb=" N PRO B 289 " pdb=" CA PRO B 289 " pdb=" CB PRO B 289 " ideal model delta sigma weight residual 103.08 111.55 -8.47 9.70e-01 1.06e+00 7.62e+01 angle pdb=" C TYR A 766 " pdb=" CA TYR A 766 " pdb=" CB TYR A 766 " ideal model delta sigma weight residual 109.51 125.49 -15.98 1.85e+00 2.92e-01 7.46e+01 angle pdb=" N PRO B1356 " pdb=" CA PRO B1356 " pdb=" CB PRO B1356 " ideal model delta sigma weight residual 103.25 112.24 -8.99 1.05e+00 9.07e-01 7.33e+01 angle pdb=" N PRO B1049 " pdb=" CA PRO B1049 " pdb=" CB PRO B1049 " ideal model delta sigma weight residual 103.25 111.50 -8.25 1.05e+00 9.07e-01 6.17e+01 ... (remaining 28990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 12627 33.45 - 66.90: 420 66.90 - 100.35: 36 100.35 - 133.80: 3 133.80 - 167.25: 6 Dihedral angle restraints: 13092 sinusoidal: 5755 harmonic: 7337 Sorted by residual: dihedral pdb=" O4' U C 16 " pdb=" C1' U C 16 " pdb=" N1 U C 16 " pdb=" C2 U C 16 " ideal model delta sinusoidal sigma weight residual -160.00 7.25 -167.25 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 200.00 43.69 156.31 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual 200.00 53.92 146.08 1 1.50e+01 4.44e-03 7.81e+01 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2994 0.102 - 0.203: 155 0.203 - 0.305: 12 0.305 - 0.407: 1 0.407 - 0.508: 1 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CA TYR A 766 " pdb=" N TYR A 766 " pdb=" C TYR A 766 " pdb=" CB TYR A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" C1' U C 27 " pdb=" O4' U C 27 " pdb=" C2' U C 27 " pdb=" N1 U C 27 " both_signs ideal model delta sigma weight residual False 2.45 2.08 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA PRO B1345 " pdb=" N PRO B1345 " pdb=" C PRO B1345 " pdb=" CB PRO B1345 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3160 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1096 " 0.081 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO B1097 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO B1097 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO B1097 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B1430 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO B1431 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B1431 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1431 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1521 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ASP B1521 " -0.065 2.00e-02 2.50e+03 pdb=" O ASP B1521 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS B1522 " 0.022 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3052 2.76 - 3.29: 19266 3.29 - 3.83: 32250 3.83 - 4.36: 37394 4.36 - 4.90: 65422 Nonbonded interactions: 157384 Sorted by model distance: nonbonded pdb=" NZ LYS A 310 " pdb=" OG1 THR A 313 " model vdw 2.223 2.520 nonbonded pdb=" O ARG A 208 " pdb=" OG1 THR A 212 " model vdw 2.228 2.440 nonbonded pdb=" O LYS B1446 " pdb=" NE2 GLN B1450 " model vdw 2.230 2.520 nonbonded pdb=" O PRO B 923 " pdb=" OH TYR B1556 " model vdw 2.237 2.440 nonbonded pdb=" OG SER B 573 " pdb=" OD1 ASP B 575 " model vdw 2.239 2.440 ... (remaining 157379 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 74.510 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.003 0.084 21377 Z= 0.207 Angle : 0.652 15.983 28995 Z= 0.405 Chirality : 0.047 0.508 3163 Planarity : 0.005 0.119 3599 Dihedral : 16.618 167.248 8336 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.54 % Favored : 91.70 % Rotamer: Outliers : 0.81 % Allowed : 0.43 % Favored : 98.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2497 helix: 2.07 (0.18), residues: 898 sheet: 0.07 (0.32), residues: 302 loop : -1.58 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1788 HIS 0.007 0.001 HIS A 657 PHE 0.017 0.001 PHE B 201 TYR 0.019 0.001 TYR B1444 ARG 0.006 0.000 ARG B 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.7060 (t80) REVERT: B 555 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6978 (p0) REVERT: B 1128 MET cc_start: 0.3967 (ttm) cc_final: 0.3517 (mmm) outliers start: 15 outliers final: 6 residues processed: 193 average time/residue: 0.3554 time to fit residues: 104.9706 Evaluate side-chains 147 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1528 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN B 446 GLN B 537 HIS ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1739 ASN ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21377 Z= 0.158 Angle : 0.539 12.009 28995 Z= 0.276 Chirality : 0.040 0.240 3163 Planarity : 0.004 0.084 3599 Dihedral : 13.234 164.018 3344 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.58 % Favored : 91.94 % Rotamer: Outliers : 1.04 % Allowed : 5.41 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2497 helix: 2.14 (0.18), residues: 905 sheet: 0.12 (0.32), residues: 298 loop : -1.58 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1788 HIS 0.003 0.001 HIS B 754 PHE 0.020 0.001 PHE B1457 TYR 0.019 0.001 TYR A 454 ARG 0.006 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 2.288 Fit side-chains REVERT: B 394 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7159 (t80) REVERT: B 395 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8410 (mm) outliers start: 20 outliers final: 8 residues processed: 158 average time/residue: 0.3380 time to fit residues: 83.7542 Evaluate side-chains 147 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 946 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 0.0060 chunk 191 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 185 optimal weight: 20.0000 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21377 Z= 0.142 Angle : 0.512 9.627 28995 Z= 0.260 Chirality : 0.039 0.199 3163 Planarity : 0.004 0.073 3599 Dihedral : 13.012 163.394 3328 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.42 % Favored : 92.10 % Rotamer: Outliers : 0.81 % Allowed : 7.41 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.17), residues: 2497 helix: 2.24 (0.18), residues: 894 sheet: 0.39 (0.33), residues: 297 loop : -1.60 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1788 HIS 0.005 0.001 HIS B1371 PHE 0.018 0.001 PHE B 201 TYR 0.014 0.001 TYR B1444 ARG 0.006 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 2.359 Fit side-chains REVERT: B 394 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7141 (t80) outliers start: 15 outliers final: 8 residues processed: 155 average time/residue: 0.3661 time to fit residues: 87.9029 Evaluate side-chains 144 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 231 optimal weight: 0.0050 chunk 245 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 446 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21377 Z= 0.177 Angle : 0.528 11.559 28995 Z= 0.269 Chirality : 0.040 0.203 3163 Planarity : 0.004 0.068 3599 Dihedral : 13.030 165.124 3324 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.82 % Favored : 91.58 % Rotamer: Outliers : 1.14 % Allowed : 8.74 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2497 helix: 2.20 (0.18), residues: 892 sheet: 0.28 (0.33), residues: 302 loop : -1.63 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1788 HIS 0.004 0.001 HIS B1610 PHE 0.020 0.001 PHE B 201 TYR 0.013 0.001 TYR A 685 ARG 0.006 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: B 394 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 510 CYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7025 (p) REVERT: B 895 MET cc_start: 0.5483 (tpt) cc_final: 0.5207 (tpt) REVERT: B 1520 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6148 (tp) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.3550 time to fit residues: 84.5375 Evaluate side-chains 150 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1507 ASP Chi-restraints excluded: chain B residue 1520 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 50.0000 chunk 139 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 chunk 169 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.0670 chunk 220 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 446 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21377 Z= 0.203 Angle : 0.545 11.283 28995 Z= 0.278 Chirality : 0.040 0.226 3163 Planarity : 0.004 0.065 3599 Dihedral : 13.056 165.535 3324 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.06 % Favored : 91.34 % Rotamer: Outliers : 1.33 % Allowed : 9.50 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2497 helix: 2.14 (0.18), residues: 893 sheet: 0.07 (0.32), residues: 304 loop : -1.66 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1788 HIS 0.004 0.001 HIS B1610 PHE 0.022 0.001 PHE B 201 TYR 0.016 0.001 TYR A 75 ARG 0.005 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 2.296 Fit side-chains revert: symmetry clash REVERT: B 394 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7067 (t80) REVERT: B 510 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7078 (p) REVERT: B 895 MET cc_start: 0.5547 (tpt) cc_final: 0.5289 (tpt) REVERT: B 1520 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6177 (tp) outliers start: 26 outliers final: 14 residues processed: 158 average time/residue: 0.3388 time to fit residues: 82.8070 Evaluate side-chains 150 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1507 ASP Chi-restraints excluded: chain B residue 1520 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 204 optimal weight: 40.0000 chunk 113 optimal weight: 0.0020 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 159 ASN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 446 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21377 Z= 0.219 Angle : 0.553 11.023 28995 Z= 0.282 Chirality : 0.041 0.289 3163 Planarity : 0.004 0.063 3599 Dihedral : 13.114 168.161 3324 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.10 % Favored : 91.30 % Rotamer: Outliers : 1.42 % Allowed : 9.73 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.17), residues: 2497 helix: 2.04 (0.18), residues: 900 sheet: -0.05 (0.32), residues: 312 loop : -1.75 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1788 HIS 0.005 0.001 HIS B 537 PHE 0.022 0.001 PHE B 201 TYR 0.017 0.001 TYR A 75 ARG 0.005 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 2.535 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5367 (mtp) REVERT: B 325 LEU cc_start: 0.8395 (mm) cc_final: 0.8007 (mm) REVERT: B 394 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.7071 (t80) REVERT: B 510 CYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7144 (p) REVERT: B 895 MET cc_start: 0.5594 (tpt) cc_final: 0.5347 (tpt) REVERT: B 1520 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6258 (tp) outliers start: 28 outliers final: 19 residues processed: 154 average time/residue: 0.3747 time to fit residues: 88.6488 Evaluate side-chains 154 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1371 HIS Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1442 GLN Chi-restraints excluded: chain B residue 1507 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1537 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 113 optimal weight: 0.0070 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 446 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21377 Z= 0.137 Angle : 0.513 10.667 28995 Z= 0.260 Chirality : 0.039 0.272 3163 Planarity : 0.004 0.062 3599 Dihedral : 12.939 167.287 3324 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.78 % Favored : 92.66 % Rotamer: Outliers : 1.04 % Allowed : 10.68 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2497 helix: 2.18 (0.18), residues: 893 sheet: 0.12 (0.32), residues: 306 loop : -1.66 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 375 HIS 0.002 0.000 HIS B1610 PHE 0.017 0.001 PHE B 201 TYR 0.013 0.001 TYR A 75 ARG 0.004 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: B 394 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7111 (t80) REVERT: B 895 MET cc_start: 0.5548 (tpt) cc_final: 0.5288 (tpt) REVERT: B 1438 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6712 (mmtm) REVERT: B 1520 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6156 (tp) outliers start: 20 outliers final: 14 residues processed: 158 average time/residue: 0.3505 time to fit residues: 85.7207 Evaluate side-chains 150 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1442 GLN Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1537 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 446 GLN B1430 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21377 Z= 0.187 Angle : 0.546 12.557 28995 Z= 0.277 Chirality : 0.040 0.257 3163 Planarity : 0.004 0.061 3599 Dihedral : 12.972 166.752 3324 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.74 % Favored : 91.74 % Rotamer: Outliers : 1.19 % Allowed : 11.02 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2497 helix: 2.11 (0.18), residues: 899 sheet: 0.09 (0.32), residues: 304 loop : -1.71 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 375 HIS 0.003 0.001 HIS B1610 PHE 0.020 0.001 PHE B 201 TYR 0.017 0.001 TYR A 685 ARG 0.005 0.000 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 2.294 Fit side-chains REVERT: B 325 LEU cc_start: 0.8370 (mm) cc_final: 0.7984 (mm) REVERT: B 394 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7123 (t80) REVERT: B 895 MET cc_start: 0.5609 (tpt) cc_final: 0.5355 (tpt) REVERT: B 1011 MET cc_start: 0.7699 (mtp) cc_final: 0.7493 (mtp) REVERT: B 1520 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6111 (tp) outliers start: 23 outliers final: 17 residues processed: 153 average time/residue: 0.3408 time to fit residues: 81.2636 Evaluate side-chains 152 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1442 GLN Chi-restraints excluded: chain B residue 1507 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1537 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 206 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 364 ASN B 400 GLN B 446 GLN B1290 HIS ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1739 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21377 Z= 0.386 Angle : 0.684 13.146 28995 Z= 0.350 Chirality : 0.045 0.344 3163 Planarity : 0.005 0.061 3599 Dihedral : 13.375 178.170 3324 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.98 % Favored : 90.50 % Rotamer: Outliers : 1.28 % Allowed : 11.21 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2497 helix: 1.67 (0.18), residues: 901 sheet: -0.23 (0.32), residues: 295 loop : -1.91 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 375 HIS 0.005 0.002 HIS B1539 PHE 0.026 0.002 PHE B1437 TYR 0.025 0.002 TYR B 49 ARG 0.007 0.001 ARG B1777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 2.288 Fit side-chains REVERT: A 234 MET cc_start: 0.7835 (mtt) cc_final: 0.7509 (mtt) REVERT: A 788 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6691 (mtmt) REVERT: B 394 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.7070 (t80) REVERT: B 895 MET cc_start: 0.5757 (tpt) cc_final: 0.5540 (tpt) REVERT: B 1438 LYS cc_start: 0.7184 (mmtt) cc_final: 0.6626 (mmtm) REVERT: B 1520 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6503 (tp) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.3832 time to fit residues: 90.1898 Evaluate side-chains 146 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1507 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1524 LYS Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21377 Z= 0.239 Angle : 0.608 14.506 28995 Z= 0.309 Chirality : 0.042 0.275 3163 Planarity : 0.005 0.098 3599 Dihedral : 13.275 179.763 3324 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.14 % Favored : 91.34 % Rotamer: Outliers : 1.23 % Allowed : 11.78 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2497 helix: 1.76 (0.18), residues: 904 sheet: -0.10 (0.32), residues: 287 loop : -1.90 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 375 HIS 0.005 0.001 HIS A 657 PHE 0.025 0.001 PHE B1437 TYR 0.020 0.001 TYR A 685 ARG 0.005 0.000 ARG B1777 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 2.369 Fit side-chains revert: symmetry clash REVERT: A 234 MET cc_start: 0.7732 (mtt) cc_final: 0.7416 (mtt) REVERT: A 662 LYS cc_start: 0.8076 (mptt) cc_final: 0.7555 (mmtt) REVERT: A 788 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6647 (mtmt) REVERT: B 394 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.7046 (t80) REVERT: B 895 MET cc_start: 0.5755 (tpt) cc_final: 0.5518 (tpt) REVERT: B 1438 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6546 (mmtm) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.3623 time to fit residues: 81.2281 Evaluate side-chains 145 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 394 TYR Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 834 ASP Chi-restraints excluded: chain B residue 946 GLU Chi-restraints excluded: chain B residue 1375 TYR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1507 ASP Chi-restraints excluded: chain B residue 1537 PHE Chi-restraints excluded: chain B residue 1751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 0.0470 chunk 214 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1540 HIS ** 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 = 0.3971 r_free = 0.3971 target = 0.139076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100996 restraints weight = 60171.678| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.05 r_work: 0.3256 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21377 Z= 0.291 Angle : 0.635 13.711 28995 Z= 0.324 Chirality : 0.043 0.299 3163 Planarity : 0.005 0.090 3599 Dihedral : 13.304 177.888 3324 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.06 % Favored : 90.38 % Rotamer: Outliers : 1.09 % Allowed : 11.92 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2497 helix: 1.67 (0.18), residues: 903 sheet: -0.22 (0.32), residues: 295 loop : -1.96 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 375 HIS 0.004 0.001 HIS B1610 PHE 0.027 0.002 PHE B1437 TYR 0.023 0.002 TYR A 685 ARG 0.006 0.001 ARG B1777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.68 seconds wall clock time: 73 minutes 16.02 seconds (4396.02 seconds total)