Starting phenix.real_space_refine on Thu Feb 15 14:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a65_11666/02_2024/7a65_11666_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a65_11666/02_2024/7a65_11666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a65_11666/02_2024/7a65_11666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a65_11666/02_2024/7a65_11666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a65_11666/02_2024/7a65_11666_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a65_11666/02_2024/7a65_11666_updated.pdb" } resolution = 3.9 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= 0.002 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 50 5.16 5 C 8075 2.51 5 N 2086 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 798": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12521 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.99, per 1000 atoms: 0.56 Number of scatterers: 12521 At special positions: 0 Unit cell: (102.48, 207.48, 99.96, 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 50 16.00 O 2310 8.00 N 2086 7.00 C 8075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.3 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 16 sheets defined 48.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 36 through 39 No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 45 through 81 removed outlier: 4.504A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.693A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 157 removed outlier: 3.642A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 168 through 186 removed outlier: 4.128A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.571A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 240 through 259 removed outlier: 3.568A pdb=" N LEU A 244 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 249 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 251 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 270 through 322 removed outlier: 3.544A pdb=" N LEU A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 347 removed outlier: 4.036A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 370 removed outlier: 4.330A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.524A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 533 through 547 removed outlier: 4.703A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 700 through 740 removed outlier: 3.525A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Proline residue: A 709 - end of helix removed outlier: 4.284A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.615A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 798 Processing helix chain 'A' and resid 801 through 805 Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 812 through 853 removed outlier: 3.647A pdb=" N LEU A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 880 removed outlier: 3.946A pdb=" N ILE A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Proline residue: A 866 - end of helix Processing helix chain 'A' and resid 891 through 908 removed outlier: 3.540A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 908 " --> pdb=" O PHE A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 966 removed outlier: 4.582A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 4.457A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 994 Processing helix chain 'A' and resid 998 through 1013 Processing helix chain 'A' and resid 1077 through 1083 Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.642A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1134 removed outlier: 4.415A pdb=" N GLY A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1164 through 1166 No H-bonds generated for 'chain 'A' and resid 1164 through 1166' Processing helix chain 'A' and resid 1171 through 1173 No H-bonds generated for 'chain 'A' and resid 1171 through 1173' Processing helix chain 'A' and resid 1178 through 1192 removed outlier: 4.330A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 removed outlier: 3.902A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 No H-bonds generated for 'chain 'A' and resid 1235 through 1238' Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing sheet with id= A, first strand: chain 'A' and resid 392 through 394 Processing sheet with id= B, first strand: chain 'A' and resid 605 through 608 removed outlier: 6.509A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id= D, first strand: chain 'A' and resid 1066 through 1069 removed outlier: 6.825A pdb=" N LEU A1242 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A1069 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A1244 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1196 through 1200 removed outlier: 6.509A pdb=" N THR A1226 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU A1199 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A1228 " --> pdb=" O LEU A1199 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.267A pdb=" N LYS B 108 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 13 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU B 110 " --> pdb=" O VAL B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 90 through 95 removed outlier: 5.920A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.565A pdb=" N ASN B 142 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.257A pdb=" N TRP B 153 " --> pdb=" O GLN B 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.403A pdb=" N THR C 116 " --> pdb=" O VAL C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 113 through 115 removed outlier: 5.777A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.635A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 157 through 160 Processing sheet with id= P, first strand: chain 'C' and resid 175 through 177 642 hydrogen bonds defined for protein. 1812 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: 4.58 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3974 1.34 - 1.46: 2940 1.46 - 1.58: 5788 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 12785 Sorted by residual: bond pdb=" C TYR A1087 " pdb=" N ASP A1088 " ideal model delta sigma weight residual 1.333 1.300 0.033 1.61e-02 3.86e+03 4.24e+00 bond pdb=" C ALA B 116 " pdb=" N ALA B 117 " ideal model delta sigma weight residual 1.339 1.246 0.093 5.57e-02 3.22e+02 2.81e+00 bond pdb=" C13 CLR A1303 " pdb=" C17 CLR A1303 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C10 CLR A1303 " pdb=" C9 CLR A1303 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" CA ALA A 260 " pdb=" CB ALA A 260 " ideal model delta sigma weight residual 1.527 1.488 0.040 2.48e-02 1.63e+03 2.56e+00 ... (remaining 12780 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.04: 240 106.04 - 113.05: 7221 113.05 - 120.06: 4336 120.06 - 127.07: 5441 127.07 - 134.08: 105 Bond angle restraints: 17343 Sorted by residual: angle pdb=" N SER A1020 " pdb=" CA SER A1020 " pdb=" C SER A1020 " ideal model delta sigma weight residual 113.97 109.29 4.68 1.28e+00 6.10e-01 1.34e+01 angle pdb=" C VAL A1273 " pdb=" CA VAL A1273 " pdb=" CB VAL A1273 " ideal model delta sigma weight residual 111.71 108.72 2.99 8.50e-01 1.38e+00 1.24e+01 angle pdb=" N VAL A 592 " pdb=" CA VAL A 592 " pdb=" C VAL A 592 " ideal model delta sigma weight residual 112.96 109.75 3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" C TYR A1087 " pdb=" N ASP A1088 " pdb=" CA ASP A1088 " ideal model delta sigma weight residual 121.83 116.94 4.89 1.56e+00 4.11e-01 9.83e+00 angle pdb=" C SER B 68 " pdb=" N GLY B 69 " pdb=" CA GLY B 69 " ideal model delta sigma weight residual 122.73 119.95 2.78 9.30e-01 1.16e+00 8.91e+00 ... (remaining 17338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 7188 16.20 - 32.39: 536 32.39 - 48.59: 134 48.59 - 64.79: 34 64.79 - 80.98: 6 Dihedral angle restraints: 7898 sinusoidal: 3312 harmonic: 4586 Sorted by residual: dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N ILE B 56 " pdb=" CA ILE B 56 " ideal model delta harmonic sigma weight residual 180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN B 216 " pdb=" C ASN B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ARG B 217 " pdb=" C ARG B 217 " pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1656 0.059 - 0.119: 299 0.119 - 0.178: 39 0.178 - 0.237: 6 0.237 - 0.296: 6 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C13 CLR A1300 " pdb=" C12 CLR A1300 " pdb=" C14 CLR A1300 " pdb=" C17 CLR A1300 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C13 CLR A1305 " pdb=" C12 CLR A1305 " pdb=" C14 CLR A1305 " pdb=" C17 CLR A1305 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C13 CLR A1303 " pdb=" C12 CLR A1303 " pdb=" C14 CLR A1303 " pdb=" C17 CLR A1303 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2003 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 48 " 0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 49 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 99 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 100 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C THR A 173 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 173 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 174 " -0.010 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1479 2.74 - 3.28: 12836 3.28 - 3.82: 20241 3.82 - 4.36: 23841 4.36 - 4.90: 40450 Nonbonded interactions: 98847 Sorted by model distance: nonbonded pdb=" O PHE A 623 " pdb=" OG1 THR A 627 " model vdw 2.200 2.440 nonbonded pdb=" O SER A1272 " pdb=" OG SER A1272 " model vdw 2.202 2.440 nonbonded pdb=" O PHE C 29 " pdb=" NH2 ARG C 72 " model vdw 2.218 2.520 nonbonded pdb=" O ALA A 233 " pdb=" OG SER A 237 " model vdw 2.218 2.440 nonbonded pdb=" O SER A 43 " pdb=" NZ LYS A 48 " model vdw 2.230 2.520 ... (remaining 98842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 12.620 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.390 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.007 0.093 12785 Z= 0.476 Angle : 0.788 8.845 17343 Z= 0.432 Chirality : 0.049 0.296 2006 Planarity : 0.004 0.052 2156 Dihedral : 12.706 80.982 4943 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.72 % Allowed : 7.72 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.19), residues: 1584 helix: -1.10 (0.16), residues: 759 sheet: -0.71 (0.29), residues: 283 loop : -2.42 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 160 HIS 0.004 0.001 HIS A 166 PHE 0.020 0.002 PHE B 94 TYR 0.024 0.002 TYR C 95 ARG 0.004 0.001 ARG A 798 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 282 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7992 (t60) cc_final: 0.7673 (t60) REVERT: A 499 GLU cc_start: 0.6276 (mt-10) cc_final: 0.6025 (mm-30) REVERT: A 514 MET cc_start: 0.5423 (mtm) cc_final: 0.4637 (tmm) REVERT: A 799 GLN cc_start: 0.7907 (mm110) cc_final: 0.7673 (mm-40) REVERT: A 816 THR cc_start: 0.7941 (m) cc_final: 0.7392 (t) REVERT: A 1183 ARG cc_start: 0.5891 (mtm180) cc_final: 0.5521 (mtp85) REVERT: A 1270 MET cc_start: -0.0551 (OUTLIER) cc_final: -0.0877 (mtt) REVERT: B 171 GLN cc_start: 0.8046 (tt0) cc_final: 0.6997 (tt0) REVERT: C 25 SER cc_start: 0.8624 (p) cc_final: 0.8135 (t) REVERT: C 121 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (ptmm) REVERT: C 173 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.7800 (Cg_exo) outliers start: 23 outliers final: 7 residues processed: 297 average time/residue: 0.2997 time to fit residues: 121.0993 Evaluate side-chains 159 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 1270 MET Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 398 HIS A 438 GLN A 462 ASN A 475 GLN A 612 HIS A 704 ASN A 750 GLN A 799 GLN A 903 ASN A 914 GLN A 946 GLN A 966 HIS A1054 GLN A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1248 ASN B 18 GLN B 129 GLN B 171 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12785 Z= 0.174 Angle : 0.573 7.967 17343 Z= 0.293 Chirality : 0.041 0.160 2006 Planarity : 0.004 0.037 2156 Dihedral : 6.503 59.332 2131 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.70 % Allowed : 14.31 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1584 helix: 0.70 (0.18), residues: 764 sheet: -0.05 (0.31), residues: 278 loop : -1.78 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 698 HIS 0.004 0.001 HIS A 966 PHE 0.021 0.002 PHE A 200 TYR 0.014 0.001 TYR A 118 ARG 0.006 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7774 (t60) cc_final: 0.7300 (t60) REVERT: A 393 GLU cc_start: 0.5844 (tm-30) cc_final: 0.5601 (tm-30) REVERT: A 514 MET cc_start: 0.5260 (mtm) cc_final: 0.4555 (tmm) REVERT: A 616 MET cc_start: 0.1390 (mmp) cc_final: 0.0731 (mmm) REVERT: A 799 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 811 THR cc_start: 0.4243 (m) cc_final: 0.4015 (m) REVERT: A 948 MET cc_start: 0.7551 (tpt) cc_final: 0.7328 (tpp) REVERT: A 949 MET cc_start: 0.8171 (tmm) cc_final: 0.7647 (tpt) REVERT: A 1270 MET cc_start: -0.0000 (tpt) cc_final: -0.0610 (mtt) REVERT: C 173 PRO cc_start: 0.7794 (Cg_endo) cc_final: 0.7479 (Cg_exo) outliers start: 36 outliers final: 16 residues processed: 210 average time/residue: 0.2338 time to fit residues: 72.3229 Evaluate side-chains 152 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 119 optimal weight: 0.3980 chunk 97 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN B 18 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12785 Z= 0.220 Angle : 0.578 9.227 17343 Z= 0.300 Chirality : 0.042 0.140 2006 Planarity : 0.004 0.040 2156 Dihedral : 5.952 56.707 2110 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.57 % Allowed : 16.78 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1584 helix: 1.12 (0.19), residues: 766 sheet: 0.34 (0.32), residues: 275 loop : -1.54 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 855 HIS 0.004 0.001 HIS A 936 PHE 0.024 0.002 PHE A 200 TYR 0.018 0.002 TYR B 54 ARG 0.004 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 163 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7914 (t60) cc_final: 0.7563 (t60) REVERT: A 393 GLU cc_start: 0.5835 (tm-30) cc_final: 0.5597 (tm-30) REVERT: A 514 MET cc_start: 0.5345 (mtm) cc_final: 0.4799 (tmm) REVERT: A 799 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7714 (mm-40) REVERT: A 948 MET cc_start: 0.7598 (tpt) cc_final: 0.7347 (tpp) REVERT: A 949 MET cc_start: 0.8179 (tmm) cc_final: 0.7579 (tpt) REVERT: A 1010 MET cc_start: 0.5604 (ptt) cc_final: 0.4766 (ttp) REVERT: A 1270 MET cc_start: -0.0037 (tpt) cc_final: -0.0521 (mtt) REVERT: B 95 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8208 (pp30) REVERT: B 171 GLN cc_start: 0.7321 (tt0) cc_final: 0.6805 (tt0) outliers start: 61 outliers final: 36 residues processed: 209 average time/residue: 0.2268 time to fit residues: 69.7696 Evaluate side-chains 169 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 0.0870 chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS A 570 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12785 Z= 0.329 Angle : 0.678 10.882 17343 Z= 0.353 Chirality : 0.044 0.147 2006 Planarity : 0.004 0.037 2156 Dihedral : 6.190 58.093 2110 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.47 % Allowed : 18.35 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1584 helix: 0.82 (0.19), residues: 757 sheet: 0.23 (0.32), residues: 272 loop : -1.68 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 162 HIS 0.006 0.001 HIS A 936 PHE 0.021 0.002 PHE A 200 TYR 0.020 0.002 TYR A 50 ARG 0.004 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 136 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 393 GLU cc_start: 0.5603 (tm-30) cc_final: 0.5284 (tm-30) REVERT: A 514 MET cc_start: 0.5596 (mtm) cc_final: 0.5106 (tmm) REVERT: A 770 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: A 799 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7757 (mm-40) REVERT: A 811 THR cc_start: 0.5748 (m) cc_final: 0.5544 (m) REVERT: A 814 LEU cc_start: 0.8380 (mt) cc_final: 0.7957 (mt) REVERT: A 948 MET cc_start: 0.7784 (tpt) cc_final: 0.7513 (tpp) REVERT: A 1010 MET cc_start: 0.5733 (ptt) cc_final: 0.4839 (ttp) REVERT: A 1270 MET cc_start: -0.0333 (tpt) cc_final: -0.0793 (mtt) REVERT: B 95 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8247 (pp30) REVERT: C 25 SER cc_start: 0.8538 (p) cc_final: 0.8275 (t) outliers start: 73 outliers final: 52 residues processed: 193 average time/residue: 0.2104 time to fit residues: 62.1994 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 118 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.0470 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 GLN A1195 HIS B 58 ASN B 142 ASN B 143 ASN C 170 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12785 Z= 0.166 Angle : 0.544 9.106 17343 Z= 0.280 Chirality : 0.040 0.145 2006 Planarity : 0.003 0.038 2156 Dihedral : 5.378 57.098 2107 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.75 % Allowed : 21.35 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1584 helix: 1.36 (0.19), residues: 767 sheet: 0.45 (0.32), residues: 277 loop : -1.42 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 708 HIS 0.004 0.001 HIS C 170 PHE 0.028 0.001 PHE B 123 TYR 0.018 0.001 TYR A 378 ARG 0.004 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7573 (mtp) cc_final: 0.7203 (mtt) REVERT: A 155 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 156 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8266 (mmp) REVERT: A 514 MET cc_start: 0.5570 (mtm) cc_final: 0.5114 (tmm) REVERT: A 521 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: A 543 ARG cc_start: 0.7203 (ttp-170) cc_final: 0.6427 (ttt-90) REVERT: A 616 MET cc_start: 0.3243 (mpp) cc_final: 0.2985 (mpp) REVERT: A 796 MET cc_start: 0.8056 (mtt) cc_final: 0.7499 (mtm) REVERT: A 799 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7734 (mm-40) REVERT: A 811 THR cc_start: 0.5504 (m) cc_final: 0.5265 (m) REVERT: A 814 LEU cc_start: 0.8304 (mt) cc_final: 0.7829 (mt) REVERT: A 878 MET cc_start: 0.4609 (ttt) cc_final: 0.4404 (ptm) REVERT: A 920 TYR cc_start: 0.7919 (t80) cc_final: 0.7621 (t80) REVERT: A 948 MET cc_start: 0.7621 (tpt) cc_final: 0.7304 (tpp) REVERT: A 1010 MET cc_start: 0.5842 (ptt) cc_final: 0.4780 (ttp) REVERT: A 1270 MET cc_start: 0.0185 (tpt) cc_final: -0.0441 (mtt) REVERT: B 128 GLU cc_start: 0.6471 (mp0) cc_final: 0.6264 (mp0) REVERT: C 25 SER cc_start: 0.8445 (p) cc_final: 0.8151 (t) outliers start: 50 outliers final: 29 residues processed: 176 average time/residue: 0.2387 time to fit residues: 63.2039 Evaluate side-chains 152 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 508 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12785 Z= 0.206 Angle : 0.565 9.917 17343 Z= 0.290 Chirality : 0.041 0.156 2006 Planarity : 0.003 0.037 2156 Dihedral : 5.264 53.635 2107 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.34 % Allowed : 21.27 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1584 helix: 1.41 (0.19), residues: 770 sheet: 0.51 (0.32), residues: 273 loop : -1.41 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.003 0.001 HIS A 936 PHE 0.030 0.002 PHE B 123 TYR 0.016 0.001 TYR B 54 ARG 0.003 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 124 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 155 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 156 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8284 (mmp) REVERT: A 514 MET cc_start: 0.5701 (mtm) cc_final: 0.5165 (tmm) REVERT: A 521 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6605 (m-30) REVERT: A 543 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.6544 (ttt-90) REVERT: A 770 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: A 796 MET cc_start: 0.8067 (mtt) cc_final: 0.7506 (mtm) REVERT: A 799 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7766 (mm-40) REVERT: A 811 THR cc_start: 0.5652 (m) cc_final: 0.5397 (m) REVERT: A 814 LEU cc_start: 0.8389 (mt) cc_final: 0.7880 (mt) REVERT: A 878 MET cc_start: 0.4987 (ttt) cc_final: 0.4647 (ptm) REVERT: A 920 TYR cc_start: 0.7962 (t80) cc_final: 0.7636 (t80) REVERT: A 948 MET cc_start: 0.7652 (tpt) cc_final: 0.7290 (tpp) REVERT: A 1010 MET cc_start: 0.5907 (ptt) cc_final: 0.4856 (ttp) REVERT: A 1027 MET cc_start: 0.0015 (mmp) cc_final: -0.0296 (mmp) REVERT: A 1270 MET cc_start: -0.0018 (tpt) cc_final: -0.0491 (mtt) REVERT: B 95 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8048 (pp30) outliers start: 58 outliers final: 40 residues processed: 168 average time/residue: 0.2155 time to fit residues: 55.4287 Evaluate side-chains 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 12785 Z= 0.162 Angle : 0.531 8.437 17343 Z= 0.271 Chirality : 0.040 0.147 2006 Planarity : 0.003 0.067 2156 Dihedral : 5.022 48.434 2107 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.60 % Allowed : 22.17 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1584 helix: 1.66 (0.19), residues: 772 sheet: 0.68 (0.33), residues: 266 loop : -1.28 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.007 0.001 HIS A 612 PHE 0.023 0.001 PHE A 200 TYR 0.013 0.001 TYR B 54 ARG 0.003 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 155 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8526 (tt) REVERT: A 156 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8184 (mmp) REVERT: A 450 MET cc_start: 0.6669 (mmt) cc_final: 0.6407 (mmp) REVERT: A 514 MET cc_start: 0.5611 (mtm) cc_final: 0.5056 (tmm) REVERT: A 521 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: A 543 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.6532 (ttt-90) REVERT: A 795 SER cc_start: 0.9008 (m) cc_final: 0.8605 (p) REVERT: A 796 MET cc_start: 0.8074 (mtt) cc_final: 0.7490 (mtm) REVERT: A 799 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7708 (mm-40) REVERT: A 811 THR cc_start: 0.5660 (m) cc_final: 0.5422 (m) REVERT: A 814 LEU cc_start: 0.8351 (mt) cc_final: 0.7833 (mt) REVERT: A 878 MET cc_start: 0.4932 (ttt) cc_final: 0.4526 (ttt) REVERT: A 891 GLU cc_start: 0.7306 (tt0) cc_final: 0.6459 (pp20) REVERT: A 920 TYR cc_start: 0.7848 (t80) cc_final: 0.7486 (t80) REVERT: A 1270 MET cc_start: 0.0304 (tpt) cc_final: -0.0208 (mtt) REVERT: B 110 GLU cc_start: 0.7553 (tp30) cc_final: 0.7131 (tp30) outliers start: 48 outliers final: 38 residues processed: 166 average time/residue: 0.2223 time to fit residues: 55.5940 Evaluate side-chains 158 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12785 Z= 0.237 Angle : 0.599 10.085 17343 Z= 0.308 Chirality : 0.042 0.145 2006 Planarity : 0.004 0.064 2156 Dihedral : 5.325 49.637 2107 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.57 % Allowed : 21.72 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1584 helix: 1.47 (0.19), residues: 765 sheet: 0.57 (0.33), residues: 267 loop : -1.33 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 153 HIS 0.008 0.001 HIS A 612 PHE 0.037 0.002 PHE B 123 TYR 0.020 0.002 TYR B 54 ARG 0.004 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 126 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 155 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 514 MET cc_start: 0.5724 (mtm) cc_final: 0.5226 (tmm) REVERT: A 521 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: A 770 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: A 796 MET cc_start: 0.8093 (mtt) cc_final: 0.7662 (mtm) REVERT: A 799 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7733 (mm-40) REVERT: A 814 LEU cc_start: 0.8382 (mt) cc_final: 0.8027 (mt) REVERT: A 920 TYR cc_start: 0.8002 (t80) cc_final: 0.7642 (t80) REVERT: A 948 MET cc_start: 0.7421 (tpp) cc_final: 0.7091 (tpp) REVERT: A 1270 MET cc_start: 0.0165 (tpt) cc_final: -0.0334 (mtt) REVERT: B 95 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: B 110 GLU cc_start: 0.7568 (tp30) cc_final: 0.7083 (tp30) REVERT: C 25 SER cc_start: 0.8546 (p) cc_final: 0.8253 (t) REVERT: C 157 THR cc_start: 0.8228 (m) cc_final: 0.8014 (p) outliers start: 61 outliers final: 44 residues processed: 173 average time/residue: 0.2283 time to fit residues: 60.7961 Evaluate side-chains 165 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.3980 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 93 optimal weight: 0.0270 chunk 150 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12785 Z= 0.157 Angle : 0.538 8.449 17343 Z= 0.274 Chirality : 0.040 0.134 2006 Planarity : 0.003 0.055 2156 Dihedral : 4.964 51.647 2107 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.52 % Allowed : 22.77 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1584 helix: 1.75 (0.19), residues: 769 sheet: 0.77 (0.34), residues: 256 loop : -1.18 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 708 HIS 0.003 0.001 HIS A 612 PHE 0.024 0.001 PHE B 123 TYR 0.019 0.001 TYR C 128 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 155 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8590 (tt) REVERT: A 514 MET cc_start: 0.5665 (mtm) cc_final: 0.5258 (tmm) REVERT: A 521 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: A 543 ARG cc_start: 0.7242 (ttp-170) cc_final: 0.6474 (ttt-90) REVERT: A 770 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: A 795 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 796 MET cc_start: 0.8081 (mtt) cc_final: 0.7505 (mtm) REVERT: A 799 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7693 (mm-40) REVERT: A 814 LEU cc_start: 0.8379 (mt) cc_final: 0.7842 (mt) REVERT: A 891 GLU cc_start: 0.7247 (tt0) cc_final: 0.6406 (pp20) REVERT: A 920 TYR cc_start: 0.7817 (t80) cc_final: 0.7481 (t80) REVERT: A 949 MET cc_start: 0.8105 (tmm) cc_final: 0.7682 (tpt) REVERT: A 953 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 1270 MET cc_start: 0.0215 (tpt) cc_final: -0.0318 (mtt) REVERT: B 110 GLU cc_start: 0.7518 (tp30) cc_final: 0.7058 (tp30) REVERT: C 157 THR cc_start: 0.8182 (m) cc_final: 0.7963 (p) outliers start: 47 outliers final: 35 residues processed: 172 average time/residue: 0.2347 time to fit residues: 59.9911 Evaluate side-chains 164 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12785 Z= 0.187 Angle : 0.563 7.862 17343 Z= 0.285 Chirality : 0.040 0.141 2006 Planarity : 0.003 0.049 2156 Dihedral : 4.929 52.321 2107 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.22 % Allowed : 23.07 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1584 helix: 1.74 (0.19), residues: 769 sheet: 0.71 (0.33), residues: 267 loop : -1.19 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 708 HIS 0.003 0.001 HIS A1112 PHE 0.025 0.001 PHE A 200 TYR 0.020 0.001 TYR C 128 ARG 0.006 0.000 ARG B 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS B 220 " (corrupted residue). Skipping it. REVERT: A 155 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 514 MET cc_start: 0.5727 (mtm) cc_final: 0.5433 (tmm) REVERT: A 521 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6605 (m-30) REVERT: A 770 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: A 795 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8607 (p) REVERT: A 796 MET cc_start: 0.8069 (mtt) cc_final: 0.7575 (mtm) REVERT: A 799 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7708 (mm-40) REVERT: A 814 LEU cc_start: 0.8407 (mt) cc_final: 0.7959 (mt) REVERT: A 891 GLU cc_start: 0.7309 (tt0) cc_final: 0.6443 (pp20) REVERT: A 920 TYR cc_start: 0.7870 (t80) cc_final: 0.7536 (t80) REVERT: A 949 MET cc_start: 0.8148 (tmm) cc_final: 0.7685 (tpt) REVERT: A 953 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6535 (t80) REVERT: A 1270 MET cc_start: 0.0151 (tpt) cc_final: -0.0396 (mtt) REVERT: B 110 GLU cc_start: 0.7533 (tp30) cc_final: 0.7070 (tp30) REVERT: C 157 THR cc_start: 0.8246 (m) cc_final: 0.7998 (p) outliers start: 43 outliers final: 36 residues processed: 154 average time/residue: 0.2140 time to fit residues: 50.9668 Evaluate side-chains 165 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 0.0470 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.147528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118707 restraints weight = 27728.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114891 restraints weight = 34953.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116311 restraints weight = 32217.323| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12785 Z= 0.153 Angle : 0.536 7.884 17343 Z= 0.270 Chirality : 0.039 0.132 2006 Planarity : 0.003 0.040 2156 Dihedral : 4.692 56.570 2107 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.15 % Allowed : 23.15 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.22), residues: 1584 helix: 1.97 (0.19), residues: 761 sheet: 0.76 (0.33), residues: 266 loop : -1.07 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 708 HIS 0.002 0.000 HIS A1112 PHE 0.025 0.001 PHE A 200 TYR 0.015 0.001 TYR C 128 ARG 0.003 0.000 ARG B 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.44 seconds wall clock time: 48 minutes 5.90 seconds (2885.90 seconds total)