Starting phenix.real_space_refine on Sun Mar 17 08:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um1_20815/03_2024/6um1_20815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um1_20815/03_2024/6um1_20815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um1_20815/03_2024/6um1_20815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um1_20815/03_2024/6um1_20815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um1_20815/03_2024/6um1_20815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um1_20815/03_2024/6um1_20815.pdb" } resolution = 3.46 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= 0.003 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 10693 2.51 5 N 2923 2.21 5 O 3382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 530": "NH1" <-> "NH2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A ARG 790": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 823": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 1048": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A ARG 1112": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1155": "OE1" <-> "OE2" Residue "A ARG 1194": "NH1" <-> "NH2" Residue "A PHE 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1221": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A ARG 1260": "NH1" <-> "NH2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A GLU 1293": "OE1" <-> "OE2" Residue "A ARG 1344": "NH1" <-> "NH2" Residue "A ARG 1365": "NH1" <-> "NH2" Residue "A ARG 1395": "NH1" <-> "NH2" Residue "A TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1448": "NH1" <-> "NH2" Residue "A ARG 1482": "NH1" <-> "NH2" Residue "A GLU 1566": "OE1" <-> "OE2" Residue "A PHE 1576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1788": "NH1" <-> "NH2" Residue "A GLU 1799": "OE1" <-> "OE2" Residue "A GLU 1807": "OE1" <-> "OE2" Residue "A ARG 1838": "NH1" <-> "NH2" Residue "A GLU 1890": "OE1" <-> "OE2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A GLU 1985": "OE1" <-> "OE2" Residue "A TYR 2012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2015": "NH1" <-> "NH2" Residue "A GLU 2050": "OE1" <-> "OE2" Residue "A ARG 2051": "NH1" <-> "NH2" Residue "A ARG 2155": "NH1" <-> "NH2" Residue "A ARG 2166": "NH1" <-> "NH2" Residue "A ARG 2179": "NH1" <-> "NH2" Residue "A ARG 2205": "NH1" <-> "NH2" Residue "A GLU 2267": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17134 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2208, 17025 Classifications: {'peptide': 2208} Link IDs: {'PTRANS': 110, 'TRANS': 2097} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.76, per 1000 atoms: 0.51 Number of scatterers: 17134 At special positions: 0 Unit cell: (174, 108, 146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3382 8.00 N 2923 7.00 C 10693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=59, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 375 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 463 " distance=2.05 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 528 " distance=2.01 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 768 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 838 " distance=2.05 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS A 918 " distance=2.03 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 930 " distance=2.04 Simple disulfide: pdb=" SG CYS A 942 " - pdb=" SG CYS A 978 " distance=2.03 Simple disulfide: pdb=" SG CYS A 984 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1086 " distance=2.03 Simple disulfide: pdb=" SG CYS A1093 " - pdb=" SG CYS A1134 " distance=2.02 Simple disulfide: pdb=" SG CYS A1143 " - pdb=" SG CYS A1151 " distance=2.04 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1199 " - pdb=" SG CYS A1226 " distance=2.04 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1271 " distance=2.04 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1291 " distance=2.00 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1358 " distance=2.01 Simple disulfide: pdb=" SG CYS A1342 " - pdb=" SG CYS A1370 " distance=2.05 Simple disulfide: pdb=" SG CYS A1378 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS A1429 " - pdb=" SG CYS A1436 " distance=2.02 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1503 " distance=2.03 Simple disulfide: pdb=" SG CYS A1485 " - pdb=" SG CYS A1515 " distance=2.04 Simple disulfide: pdb=" SG CYS A1525 " - pdb=" SG CYS A1562 " distance=2.03 Simple disulfide: pdb=" SG CYS A1568 " - pdb=" SG CYS A1575 " distance=2.03 Simple disulfide: pdb=" SG CYS A1607 " - pdb=" SG CYS A1643 " distance=2.02 Simple disulfide: pdb=" SG CYS A1623 " - pdb=" SG CYS A1655 " distance=2.03 Simple disulfide: pdb=" SG CYS A1661 " - pdb=" SG CYS A1704 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1722 " distance=2.04 Simple disulfide: pdb=" SG CYS A1759 " - pdb=" SG CYS A1792 " distance=2.04 Simple disulfide: pdb=" SG CYS A1775 " - pdb=" SG CYS A1804 " distance=2.03 Simple disulfide: pdb=" SG CYS A1813 " - pdb=" SG CYS A1848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1859 " - pdb=" SG CYS A1865 " distance=2.03 Simple disulfide: pdb=" SG CYS A1902 " - pdb=" SG CYS A1984 " distance=2.04 Simple disulfide: pdb=" SG CYS A1912 " - pdb=" SG CYS A1936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1926 " - pdb=" SG CYS A1951 " distance=2.04 Simple disulfide: pdb=" SG CYS A1966 " - pdb=" SG CYS A1996 " distance=2.04 Simple disulfide: pdb=" SG CYS A2003 " - pdb=" SG CYS A2038 " distance=2.02 Simple disulfide: pdb=" SG CYS A2048 " - pdb=" SG CYS A2055 " distance=2.03 Simple disulfide: pdb=" SG CYS A2091 " - pdb=" SG CYS A2122 " distance=2.03 Simple disulfide: pdb=" SG CYS A2105 " - pdb=" SG CYS A2134 " distance=2.03 Simple disulfide: pdb=" SG CYS A2197 " - pdb=" SG CYS A2203 " distance=2.03 Simple disulfide: pdb=" SG CYS A2241 " - pdb=" SG CYS A2275 " distance=2.03 Simple disulfide: pdb=" SG CYS A2257 " - pdb=" SG CYS A2287 " distance=2.04 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=2, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A2501 " - " ASN A 120 " " NAG A2507 " - " ASN A1030 " " NAG B 1 " - " ASN A 444 " " NAG C 1 " - " ASN A 590 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.4 seconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 50 sheets defined 2.5% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 650 through 653 Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 956 through 959 Processing helix chain 'A' and resid 1106 through 1110 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1391 through 1394 Processing helix chain 'A' and resid 1539 through 1542 Processing helix chain 'A' and resid 1673 through 1676 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.212A pdb=" N THR A 121 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 132 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 151 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU A 160 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE A 149 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 removed outlier: 4.660A pdb=" N LEU A 213 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 271 removed outlier: 6.115A pdb=" N ALA A 287 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 316 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 289 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP A 318 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR A 291 " --> pdb=" O TRP A 318 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU A 315 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.570A pdb=" N LEU A 419 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 437 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 465 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.218A pdb=" N VAL A 390 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 485 through 488 Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 removed outlier: 7.454A pdb=" N VAL A 511 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 525 Processing sheet with id=AB2, first strand: chain 'A' and resid 631 through 633 removed outlier: 6.008A pdb=" N LEU A 734 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TRP A 762 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR A 736 " --> pdb=" O TRP A 762 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR A 764 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 738 " --> pdb=" O THR A 764 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AB4, first strand: chain 'A' and resid 660 through 661 Processing sheet with id=AB5, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 866 through 867 removed outlier: 6.765A pdb=" N THR A 894 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 866 through 867 removed outlier: 7.765A pdb=" N TRP A 924 " --> pdb=" O ARG A 896 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS A 898 " --> pdb=" O TRP A 924 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR A 926 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 900 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 943 through 945 Processing sheet with id=AC1, first strand: chain 'A' and resid 964 through 966 Processing sheet with id=AC2, first strand: chain 'A' and resid 1015 through 1016 Processing sheet with id=AC3, first strand: chain 'A' and resid 1019 through 1021 removed outlier: 4.038A pdb=" N ILE A1027 " --> pdb=" O PHE A1049 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE A1080 " --> pdb=" O ILE A1046 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG A1048 " --> pdb=" O PHE A1080 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1065 through 1067 Processing sheet with id=AC5, first strand: chain 'A' and resid 1094 through 1095 Processing sheet with id=AC6, first strand: chain 'A' and resid 1128 through 1129 Processing sheet with id=AC7, first strand: chain 'A' and resid 1169 through 1170 removed outlier: 6.772A pdb=" N GLU A1215 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A1211 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A1217 " --> pdb=" O GLN A1209 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1257 through 1260 Processing sheet with id=AC9, first strand: chain 'A' and resid 1311 through 1314 removed outlier: 7.068A pdb=" N SER A1335 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N PHE A1362 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A1337 " --> pdb=" O PHE A1362 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TRP A1364 " --> pdb=" O THR A1337 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE A1339 " --> pdb=" O TRP A1364 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A1366 " --> pdb=" O PHE A1339 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A1341 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A1361 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG A1365 " --> pdb=" O ALA A1348 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA A1348 " --> pdb=" O ARG A1365 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1379 through 1381 removed outlier: 3.505A pdb=" N PHE A1380 " --> pdb=" O TYR A1388 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1400 through 1401 removed outlier: 6.057A pdb=" N VAL A1435 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1400 through 1401 removed outlier: 6.057A pdb=" N VAL A1435 " --> pdb=" O LEU A1446 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A1460 " --> pdb=" O PHE A1483 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLU A1504 " --> pdb=" O ALA A1499 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA A1499 " --> pdb=" O GLU A1504 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR A1506 " --> pdb=" O ILE A1497 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1520 through 1522 removed outlier: 3.607A pdb=" N ASN A1520 " --> pdb=" O TYR A1592 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1647 " --> pdb=" O VAL A1618 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1637 " --> pdb=" O PHE A1646 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1520 through 1522 removed outlier: 3.607A pdb=" N ASN A1520 " --> pdb=" O TYR A1592 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR A1651 " --> pdb=" O SER A1620 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A1622 " --> pdb=" O THR A1651 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1526 through 1527 Processing sheet with id=AD7, first strand: chain 'A' and resid 1547 through 1550 Processing sheet with id=AD8, first strand: chain 'A' and resid 1662 through 1665 removed outlier: 3.542A pdb=" N ASN A1665 " --> pdb=" O SER A1668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1682 through 1683 removed outlier: 3.950A pdb=" N ILE A1731 " --> pdb=" O LYS A1723 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1735 through 1736 Processing sheet with id=AE2, first strand: chain 'A' and resid 1735 through 1736 removed outlier: 7.138A pdb=" N THR A1768 " --> pdb=" O PHE A1794 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE A1796 " --> pdb=" O THR A1768 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A1770 " --> pdb=" O PHE A1796 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP A1798 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A1772 " --> pdb=" O TRP A1798 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A1800 " --> pdb=" O THR A1772 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS A1774 " --> pdb=" O THR A1800 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1834 through 1837 removed outlier: 7.260A pdb=" N GLY A1876 " --> pdb=" O ALA A1863 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1885 through 1886 removed outlier: 3.794A pdb=" N ALA A1891 " --> pdb=" O ARG A1886 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU A1985 " --> pdb=" O GLU A1980 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A1980 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR A1987 " --> pdb=" O PHE A1978 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1916 through 1918 removed outlier: 3.538A pdb=" N PHE A1916 " --> pdb=" O TYR A1923 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1935 through 1937 Processing sheet with id=AE7, first strand: chain 'A' and resid 2004 through 2006 removed outlier: 3.556A pdb=" N PHE A2005 " --> pdb=" O TYR A2012 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 2055 through 2057 Processing sheet with id=AE9, first strand: chain 'A' and resid 2074 through 2077 Processing sheet with id=AF1, first strand: chain 'A' and resid 2104 through 2105 removed outlier: 3.522A pdb=" N SER A2130 " --> pdb=" O THR A2104 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS A2125 " --> pdb=" O THR A2115 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP A2129 " --> pdb=" O ARG A2111 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A2111 " --> pdb=" O ASP A2129 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 2149 through 2150 removed outlier: 3.934A pdb=" N ARG A2155 " --> pdb=" O ASN A2150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 2173 through 2175 removed outlier: 3.905A pdb=" N THR A2175 " --> pdb=" O TYR A2182 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A2182 " --> pdb=" O THR A2175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 2200 through 2202 removed outlier: 6.757A pdb=" N GLY A2217 " --> pdb=" O SER A2201 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 2222 through 2223 removed outlier: 6.188A pdb=" N THR A2252 " --> pdb=" O PHE A2279 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP A2281 " --> pdb=" O THR A2252 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE A2254 " --> pdb=" O TRP A2281 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A2276 " --> pdb=" O THR A2272 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.38 Time building geometry restraints manager: 7.34 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: 3346 1.33 - 1.45: 4356 1.45 - 1.57: 9669 1.57 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 17524 Sorted by residual: bond pdb=" N ASP A1097 " pdb=" CA ASP A1097 " ideal model delta sigma weight residual 1.455 1.490 -0.035 7.00e-03 2.04e+04 2.46e+01 bond pdb=" N ILE A2265 " pdb=" CA ILE A2265 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.60e-03 1.35e+04 2.20e+01 bond pdb=" N ILE A2162 " pdb=" CA ILE A2162 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.08e+01 bond pdb=" N VAL A1331 " pdb=" CA VAL A1331 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 1.98e+01 bond pdb=" N ASP A1240 " pdb=" CA ASP A1240 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 ... (remaining 17519 not shown) Histogram of bond angle deviations from ideal: 92.48 - 100.95: 27 100.95 - 109.43: 2408 109.43 - 117.90: 11259 117.90 - 126.38: 9758 126.38 - 134.85: 344 Bond angle restraints: 23796 Sorted by residual: angle pdb=" C HIS A1037 " pdb=" N PRO A1038 " pdb=" CA PRO A1038 " ideal model delta sigma weight residual 119.84 133.98 -14.14 1.25e+00 6.40e-01 1.28e+02 angle pdb=" C ASP A 656 " pdb=" CA ASP A 656 " pdb=" CB ASP A 656 " ideal model delta sigma weight residual 109.55 92.90 16.65 1.68e+00 3.54e-01 9.82e+01 angle pdb=" N GLY A1425 " pdb=" CA GLY A1425 " pdb=" C GLY A1425 " ideal model delta sigma weight residual 113.18 92.48 20.70 2.37e+00 1.78e-01 7.63e+01 angle pdb=" N GLN A1423 " pdb=" CA GLN A1423 " pdb=" C GLN A1423 " ideal model delta sigma weight residual 107.73 95.01 12.72 1.80e+00 3.09e-01 5.00e+01 angle pdb=" C GLN A 515 " pdb=" N ARG A 516 " pdb=" CA ARG A 516 " ideal model delta sigma weight residual 120.38 130.70 -10.32 1.46e+00 4.69e-01 5.00e+01 ... (remaining 23791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 9950 24.08 - 48.16: 687 48.16 - 72.24: 75 72.24 - 96.33: 13 96.33 - 120.41: 8 Dihedral angle restraints: 10733 sinusoidal: 4361 harmonic: 6372 Sorted by residual: dihedral pdb=" CA PHE A1914 " pdb=" C PHE A1914 " pdb=" N PRO A1915 " pdb=" CA PRO A1915 " ideal model delta harmonic sigma weight residual -180.00 -70.55 -109.45 0 5.00e+00 4.00e-02 4.79e+02 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual 93.00 -176.91 -90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 334 " pdb=" SG CYS A 334 " pdb=" SG CYS A 375 " pdb=" CB CYS A 375 " ideal model delta sinusoidal sigma weight residual 93.00 -177.48 -89.52 1 1.00e+01 1.00e-02 9.52e+01 ... (remaining 10730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2373 0.143 - 0.286: 257 0.286 - 0.429: 6 0.429 - 0.571: 2 0.571 - 0.714: 1 Chirality restraints: 2639 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.51e+01 chirality pdb=" C1 NAG A2501 " pdb=" ND2 ASN A 120 " pdb=" C2 NAG A2501 " pdb=" O5 NAG A2501 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA ARG A 332 " pdb=" N ARG A 332 " pdb=" C ARG A 332 " pdb=" CB ARG A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 2636 not shown) Planarity restraints: 3110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 120 " -0.063 2.00e-02 2.50e+03 9.29e-02 1.08e+02 pdb=" CG ASN A 120 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 120 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 120 " 0.168 2.00e-02 2.50e+03 pdb=" C1 NAG A2501 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1037 " -0.032 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C HIS A1037 " 0.111 2.00e-02 2.50e+03 pdb=" O HIS A1037 " -0.043 2.00e-02 2.50e+03 pdb=" N PRO A1038 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A1037 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A1038 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.048 5.00e-02 4.00e+02 ... (remaining 3107 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 146 2.59 - 3.17: 13295 3.17 - 3.75: 25691 3.75 - 4.32: 35514 4.32 - 4.90: 58759 Nonbonded interactions: 133405 Sorted by model distance: nonbonded pdb=" OG SER A2053 " pdb=" O GLY A2067 " model vdw 2.014 2.440 nonbonded pdb=" O GLY A 274 " pdb=" NE2 GLN A 277 " model vdw 2.136 2.520 nonbonded pdb=" N GLY A1425 " pdb=" O GLY A1425 " model vdw 2.204 2.496 nonbonded pdb=" O TYR A 717 " pdb=" O THR A 733 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN A1321 " pdb=" C1 NAG A2508 " model vdw 2.252 3.470 ... (remaining 133400 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 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.740 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 52.870 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.014 0.061 17524 Z= 0.923 Angle : 1.829 20.704 23796 Z= 1.265 Chirality : 0.091 0.714 2639 Planarity : 0.006 0.110 3106 Dihedral : 15.713 120.408 6480 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 0.84 % Allowed : 8.61 % Favored : 90.55 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.81 % 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: -4.82 (0.14), residues: 2200 helix: -4.65 (1.01), residues: 13 sheet: -3.48 (0.17), residues: 532 loop : -3.36 (0.12), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 924 HIS 0.010 0.002 HIS A 501 PHE 0.037 0.003 PHE A1914 TYR 0.035 0.003 TYR A1373 ARG 0.016 0.001 ARG A1041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.8423 (pt) cc_final: 0.8187 (pt) REVERT: A 787 ASP cc_start: 0.6535 (t70) cc_final: 0.6332 (p0) REVERT: A 1423 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7019 (mm-40) REVERT: A 2241 CYS cc_start: -0.1611 (OUTLIER) cc_final: -0.2034 (t) outliers start: 16 outliers final: 6 residues processed: 293 average time/residue: 0.3107 time to fit residues: 135.6194 Evaluate side-chains 181 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1426 SER Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 127 GLN A 193 ASN A 311 ASN A 325 HIS A 348 GLN A 688 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 843 GLN A 857 ASN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1039 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN A1841 HIS A1887 HIS A2064 GLN A2145 ASN A2153 ASN A2227 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 17524 Z= 0.296 Angle : 0.785 13.405 23796 Z= 0.412 Chirality : 0.048 0.278 2639 Planarity : 0.006 0.115 3106 Dihedral : 9.334 66.614 2583 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.41 % Rotamer: Outliers : 3.26 % Allowed : 16.18 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.24 % 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: -4.19 (0.15), residues: 2200 helix: -4.39 (0.83), residues: 20 sheet: -2.88 (0.17), residues: 588 loop : -2.93 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 924 HIS 0.004 0.001 HIS A1650 PHE 0.029 0.002 PHE A1045 TYR 0.020 0.002 TYR A1139 ARG 0.006 0.001 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.6254 (p0) REVERT: A 599 ASP cc_start: 0.7225 (t70) cc_final: 0.6961 (t70) REVERT: A 787 ASP cc_start: 0.7008 (t70) cc_final: 0.6780 (p0) REVERT: A 1423 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6635 (mm110) REVERT: A 1547 PHE cc_start: 0.7009 (m-80) cc_final: 0.6736 (m-80) REVERT: A 1877 ARG cc_start: 0.6578 (ttt90) cc_final: 0.6365 (ttp-110) REVERT: A 2241 CYS cc_start: -0.1324 (OUTLIER) cc_final: -0.1999 (t) outliers start: 62 outliers final: 30 residues processed: 232 average time/residue: 0.2792 time to fit residues: 101.5454 Evaluate side-chains 190 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 136 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 200 optimal weight: 0.0970 chunk 216 optimal weight: 0.0980 chunk 178 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 507 ASN A 515 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 ASN A1020 GLN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1333 GLN A1665 ASN A1774 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 17524 Z= 0.216 Angle : 0.686 10.356 23796 Z= 0.361 Chirality : 0.046 0.230 2639 Planarity : 0.005 0.113 3106 Dihedral : 7.872 73.364 2576 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.45 % Favored : 90.36 % Rotamer: Outliers : 4.52 % Allowed : 17.75 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.14 % 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: -3.80 (0.15), residues: 2200 helix: -4.04 (0.91), residues: 19 sheet: -2.37 (0.19), residues: 593 loop : -2.75 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS A2282 PHE 0.026 0.002 PHE A1307 TYR 0.016 0.001 TYR A1216 ARG 0.005 0.000 ARG A1482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 189 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.6573 (OUTLIER) cc_final: 0.6127 (p0) REVERT: A 599 ASP cc_start: 0.7071 (t70) cc_final: 0.6740 (t70) REVERT: A 811 ARG cc_start: 0.7622 (mmm160) cc_final: 0.7396 (mmm160) REVERT: A 1191 PHE cc_start: 0.4269 (OUTLIER) cc_final: 0.3266 (m-80) REVERT: A 1198 GLU cc_start: 0.6181 (tp30) cc_final: 0.5961 (tp30) REVERT: A 1423 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: A 2241 CYS cc_start: -0.1051 (OUTLIER) cc_final: -0.2018 (t) outliers start: 86 outliers final: 43 residues processed: 259 average time/residue: 0.2518 time to fit residues: 104.9303 Evaluate side-chains 208 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1567 ASN Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2287 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 976 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1888 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 17524 Z= 0.364 Angle : 0.755 12.069 23796 Z= 0.395 Chirality : 0.047 0.210 2639 Planarity : 0.005 0.106 3106 Dihedral : 7.713 69.530 2576 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.18 % Favored : 87.64 % Rotamer: Outliers : 5.72 % Allowed : 18.86 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.14 % 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: -3.74 (0.16), residues: 2200 helix: -3.87 (1.17), residues: 13 sheet: -2.34 (0.19), residues: 629 loop : -2.71 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 924 HIS 0.005 0.001 HIS A 190 PHE 0.032 0.002 PHE A1078 TYR 0.020 0.002 TYR A 723 ARG 0.004 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 176 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.6591 (OUTLIER) cc_final: 0.6134 (p0) REVERT: A 599 ASP cc_start: 0.7316 (t70) cc_final: 0.7006 (t70) REVERT: A 813 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6646 (m) REVERT: A 1191 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.3903 (m-80) REVERT: A 1777 ARG cc_start: 0.3688 (tpt170) cc_final: 0.3246 (tpt170) REVERT: A 1841 HIS cc_start: 0.5153 (OUTLIER) cc_final: 0.4665 (p90) REVERT: A 1993 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6933 (ttmm) REVERT: A 2241 CYS cc_start: -0.1599 (OUTLIER) cc_final: -0.2578 (t) outliers start: 109 outliers final: 65 residues processed: 262 average time/residue: 0.2643 time to fit residues: 108.5970 Evaluate side-chains 230 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 160 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 CYS Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1841 HIS Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2109 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2287 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17524 Z= 0.313 Angle : 0.719 10.714 23796 Z= 0.377 Chirality : 0.047 0.234 2639 Planarity : 0.005 0.101 3106 Dihedral : 7.334 67.824 2572 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.09 % Favored : 88.73 % Rotamer: Outliers : 6.14 % Allowed : 20.64 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.14 % 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: -3.58 (0.16), residues: 2200 helix: -3.24 (2.34), residues: 6 sheet: -2.15 (0.20), residues: 622 loop : -2.65 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 924 HIS 0.003 0.001 HIS A 190 PHE 0.027 0.002 PHE A1078 TYR 0.027 0.002 TYR A 473 ARG 0.004 0.000 ARG A1482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 178 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.6440 (OUTLIER) cc_final: 0.5946 (p0) REVERT: A 599 ASP cc_start: 0.7181 (t70) cc_final: 0.6861 (t70) REVERT: A 813 THR cc_start: 0.6975 (OUTLIER) cc_final: 0.6774 (m) REVERT: A 1191 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.4116 (m-80) REVERT: A 1216 TYR cc_start: 0.5063 (m-80) cc_final: 0.4843 (m-80) REVERT: A 1401 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6680 (tm-30) REVERT: A 1841 HIS cc_start: 0.5128 (OUTLIER) cc_final: 0.4682 (p90) REVERT: A 2241 CYS cc_start: -0.1510 (OUTLIER) cc_final: -0.2693 (t) outliers start: 117 outliers final: 79 residues processed: 275 average time/residue: 0.2590 time to fit residues: 113.5580 Evaluate side-chains 244 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 160 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 CYS Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1841 HIS Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17524 Z= 0.211 Angle : 0.661 10.635 23796 Z= 0.347 Chirality : 0.045 0.208 2639 Planarity : 0.005 0.096 3106 Dihedral : 6.900 64.526 2572 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.59 % Favored : 89.27 % Rotamer: Outliers : 5.41 % Allowed : 21.85 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.05 % 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: -3.43 (0.16), residues: 2200 helix: -3.67 (1.88), residues: 7 sheet: -2.07 (0.20), residues: 619 loop : -2.53 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 909 PHE 0.023 0.002 PHE A1045 TYR 0.014 0.001 TYR A 72 ARG 0.004 0.000 ARG A 790 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 187 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6743 (mt) REVERT: A 599 ASP cc_start: 0.7208 (t70) cc_final: 0.6872 (t70) REVERT: A 1191 PHE cc_start: 0.4477 (OUTLIER) cc_final: 0.4142 (m-80) REVERT: A 1401 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6672 (tm-30) REVERT: A 2241 CYS cc_start: -0.1542 (OUTLIER) cc_final: -0.2563 (t) outliers start: 103 outliers final: 73 residues processed: 266 average time/residue: 0.2578 time to fit residues: 110.9236 Evaluate side-chains 244 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 168 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1436 CYS Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1661 CYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 440 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 GLN ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 17524 Z= 0.455 Angle : 0.803 11.910 23796 Z= 0.419 Chirality : 0.050 0.339 2639 Planarity : 0.006 0.093 3106 Dihedral : 7.444 63.040 2572 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.55 % Favored : 86.32 % Rotamer: Outliers : 5.93 % Allowed : 22.58 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.54 (0.16), residues: 2200 helix: -3.89 (1.73), residues: 6 sheet: -2.09 (0.20), residues: 636 loop : -2.63 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 318 HIS 0.007 0.001 HIS A 190 PHE 0.042 0.003 PHE A1078 TYR 0.024 0.002 TYR A 723 ARG 0.007 0.001 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 160 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ASP cc_start: 0.7165 (t70) cc_final: 0.6897 (t70) REVERT: A 798 PRO cc_start: 0.5385 (Cg_endo) cc_final: 0.5169 (Cg_exo) REVERT: A 1432 GLU cc_start: 0.7395 (pt0) cc_final: 0.7144 (pt0) REVERT: A 1841 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4738 (p90) REVERT: A 1993 LYS cc_start: 0.7074 (ttmt) cc_final: 0.6797 (mtpp) REVERT: A 2241 CYS cc_start: -0.1562 (OUTLIER) cc_final: -0.2682 (t) outliers start: 113 outliers final: 86 residues processed: 255 average time/residue: 0.2673 time to fit residues: 106.8946 Evaluate side-chains 230 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 142 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1841 HIS Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1884 ASP Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 GLN A2276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17524 Z= 0.276 Angle : 0.711 11.146 23796 Z= 0.371 Chirality : 0.047 0.305 2639 Planarity : 0.005 0.089 3106 Dihedral : 7.119 62.219 2572 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.91 % Favored : 89.00 % Rotamer: Outliers : 5.09 % Allowed : 23.63 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.41 (0.16), residues: 2200 helix: -3.70 (1.87), residues: 6 sheet: -1.97 (0.20), residues: 609 loop : -2.55 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1990 HIS 0.007 0.001 HIS A 909 PHE 0.027 0.002 PHE A 360 TYR 0.017 0.002 TYR A1266 ARG 0.004 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 162 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 599 ASP cc_start: 0.7183 (t70) cc_final: 0.6893 (t70) REVERT: A 798 PRO cc_start: 0.5168 (Cg_endo) cc_final: 0.4897 (Cg_exo) REVERT: A 2241 CYS cc_start: -0.1530 (OUTLIER) cc_final: -0.2673 (t) outliers start: 97 outliers final: 83 residues processed: 242 average time/residue: 0.2711 time to fit residues: 104.8643 Evaluate side-chains 240 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 155 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2149 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17524 Z= 0.363 Angle : 0.749 13.211 23796 Z= 0.390 Chirality : 0.048 0.283 2639 Planarity : 0.005 0.087 3106 Dihedral : 7.203 61.303 2572 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.50 % Favored : 86.41 % Rotamer: Outliers : 5.41 % Allowed : 23.69 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.42 (0.16), residues: 2200 helix: -3.70 (1.87), residues: 6 sheet: -2.00 (0.20), residues: 620 loop : -2.56 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 318 HIS 0.009 0.001 HIS A 909 PHE 0.032 0.002 PHE A1078 TYR 0.020 0.002 TYR A1216 ARG 0.005 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 149 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 599 ASP cc_start: 0.7249 (t70) cc_final: 0.6950 (t70) REVERT: A 798 PRO cc_start: 0.5273 (Cg_endo) cc_final: 0.5049 (Cg_exo) REVERT: A 2241 CYS cc_start: -0.1498 (OUTLIER) cc_final: -0.2599 (t) outliers start: 103 outliers final: 91 residues processed: 236 average time/residue: 0.2578 time to fit residues: 96.5956 Evaluate side-chains 236 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 143 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1364 TRP Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1661 CYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1963 ILE Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2149 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN A1037 HIS ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17524 Z= 0.233 Angle : 0.684 13.727 23796 Z= 0.355 Chirality : 0.046 0.282 2639 Planarity : 0.005 0.084 3106 Dihedral : 6.872 60.615 2572 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.73 % Favored : 89.18 % Rotamer: Outliers : 4.88 % Allowed : 24.11 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.31 (0.17), residues: 2200 helix: -3.40 (2.02), residues: 6 sheet: -1.93 (0.20), residues: 659 loop : -2.47 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 318 HIS 0.011 0.001 HIS A 909 PHE 0.027 0.002 PHE A 360 TYR 0.019 0.001 TYR A1216 ARG 0.004 0.000 ARG A 790 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 157 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6726 (mt) REVERT: A 572 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: A 599 ASP cc_start: 0.7324 (t70) cc_final: 0.6990 (t70) REVERT: A 798 PRO cc_start: 0.5191 (Cg_endo) cc_final: 0.4928 (Cg_exo) REVERT: A 2115 THR cc_start: 0.6084 (OUTLIER) cc_final: 0.5831 (m) REVERT: A 2241 CYS cc_start: -0.1445 (OUTLIER) cc_final: -0.2522 (t) outliers start: 93 outliers final: 81 residues processed: 234 average time/residue: 0.2608 time to fit residues: 97.7500 Evaluate side-chains 238 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 153 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1364 TRP Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1511 THR Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1661 CYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2149 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1534 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.188381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156608 restraints weight = 22772.571| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.05 r_work: 0.3671 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17524 Z= 0.294 Angle : 0.704 13.519 23796 Z= 0.365 Chirality : 0.047 0.277 2639 Planarity : 0.005 0.083 3106 Dihedral : 6.909 59.798 2572 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.55 % Favored : 87.36 % Rotamer: Outliers : 4.78 % Allowed : 24.37 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.31 (0.17), residues: 2200 helix: -3.48 (1.95), residues: 6 sheet: -1.95 (0.19), residues: 673 loop : -2.45 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1364 HIS 0.012 0.001 HIS A 909 PHE 0.026 0.002 PHE A 360 TYR 0.024 0.002 TYR A1216 ARG 0.006 0.000 ARG A 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3720.06 seconds wall clock time: 67 minutes 56.53 seconds (4076.53 seconds total)