Starting phenix.real_space_refine on Sat Feb 17 13:12:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lod_0936/02_2024/6lod_0936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lod_0936/02_2024/6lod_0936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lod_0936/02_2024/6lod_0936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lod_0936/02_2024/6lod_0936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lod_0936/02_2024/6lod_0936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lod_0936/02_2024/6lod_0936_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 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: 5 Type Number sf(0) Gaussians Fe 21 7.16 5 S 106 5.16 5 C 12235 2.51 5 N 3163 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Residue "F ARG 389": "NH1" <-> "NH2" Residue "F ARG 394": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18785 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "B" Number of atoms: 7176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7176 Classifications: {'peptide': 929} Link IDs: {'PTRANS': 54, 'TRANS': 874} Chain: "C" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3728 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1348 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 13, 'TRANS': 160} Chain: "E" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1253 Unusual residues: {'ACE': 1} Classifications: {'peptide': 157, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 11, 'TRANS': 145} Chain: "F" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3159 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {'EL6': 1, 'F3S': 1, 'HEC': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EL6': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7079 SG CYS B 772 43.538 61.115 46.899 1.00 15.91 S ATOM 8511 SG CYS B 952 43.881 60.933 52.417 1.00 17.30 S ATOM 7098 SG CYS B 775 48.859 61.179 48.961 1.00 14.45 S ATOM 7059 SG CYS B 769 45.917 56.117 49.454 1.00 17.48 S ATOM 8265 SG CYS B 921 54.211 68.702 54.752 1.00 12.95 S ATOM 8241 SG CYS B 918 57.243 63.355 54.147 1.00 16.80 S ATOM 7123 SG CYS B 779 55.518 66.495 50.074 1.00 15.00 S ATOM 8480 SG CYS B 948 51.626 64.350 54.163 1.00 15.65 S ATOM 7499 SG CYS B 824 61.983 60.284 55.837 1.00 13.73 S ATOM 7560 SG CYS B 832 67.745 58.412 56.225 1.00 13.23 S ATOM 7813 SG CYS B 866 65.347 56.019 52.750 1.00 13.66 S ATOM 7523 SG CYS B 827 63.465 55.132 58.459 1.00 14.54 S ATOM 7785 SG CYS B 862 71.717 60.915 50.750 1.00 14.21 S ATOM 7740 SG CYS B 856 72.937 66.254 49.471 1.00 13.76 S ATOM 7590 SG CYS B 836 74.814 63.418 54.435 1.00 13.58 S Time building chain proxies: 10.54, per 1000 atoms: 0.56 Number of scatterers: 18785 At special positions: 0 Unit cell: (159.12, 131.04, 97.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 21 26.01 S 106 16.00 O 3260 8.00 N 3163 7.00 C 12235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1106 " pdb="FE1 F3S B1106 " - pdb=" SG CYS B 862 " pdb="FE4 F3S B1106 " - pdb=" SG CYS B 836 " pdb="FE3 F3S B1106 " - pdb=" SG CYS B 856 " pdb=" SF4 B1103 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 952 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 772 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 775 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 769 " pdb=" SF4 B1104 " pdb="FE3 SF4 B1104 " - pdb=" SG CYS B 779 " pdb="FE1 SF4 B1104 " - pdb=" SG CYS B 921 " pdb="FE4 SF4 B1104 " - pdb=" SG CYS B 948 " pdb="FE2 SF4 B1104 " - pdb=" SG CYS B 918 " pdb=" SF4 B1105 " pdb="FE2 SF4 B1105 " - pdb=" SG CYS B 832 " pdb="FE4 SF4 B1105 " - pdb=" SG CYS B 827 " pdb="FE3 SF4 B1105 " - pdb=" SG CYS B 866 " pdb="FE1 SF4 B1105 " - pdb=" SG CYS B 824 " Number of angles added : 45 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 12 sheets defined 40.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.789A pdb=" N ALA A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 21 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 24 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 42 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.638A pdb=" N ALA A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.201A pdb=" N CYS A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.523A pdb=" N SER A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 215 through 218 No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.564A pdb=" N ALA B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.619A pdb=" N THR B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.603A pdb=" N THR B 217 " --> pdb=" O GLN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 243 removed outlier: 3.527A pdb=" N ALA B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.513A pdb=" N LEU B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.599A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.834A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 359 No H-bonds generated for 'chain 'B' and resid 356 through 359' Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 409 through 419 removed outlier: 3.723A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 No H-bonds generated for 'chain 'B' and resid 434 through 437' Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 463 through 466 No H-bonds generated for 'chain 'B' and resid 463 through 466' Processing helix chain 'B' and resid 507 through 515 removed outlier: 3.646A pdb=" N ASN B 512 " --> pdb=" O ILE B 508 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 530 No H-bonds generated for 'chain 'B' and resid 527 through 530' Processing helix chain 'B' and resid 539 through 549 Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 729 through 732 No H-bonds generated for 'chain 'B' and resid 729 through 732' Processing helix chain 'B' and resid 774 through 782 Processing helix chain 'B' and resid 790 through 793 No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 862 through 865 No H-bonds generated for 'chain 'B' and resid 862 through 865' Processing helix chain 'B' and resid 898 through 900 No H-bonds generated for 'chain 'B' and resid 898 through 900' Processing helix chain 'B' and resid 922 through 934 removed outlier: 3.525A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 928 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 931 " --> pdb=" O GLU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 972 No H-bonds generated for 'chain 'B' and resid 969 through 972' Processing helix chain 'C' and resid 12 through 17 removed outlier: 4.153A pdb=" N GLU C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 32 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 53 through 70 removed outlier: 3.557A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 86 through 103 removed outlier: 3.898A pdb=" N PHE C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 121 through 132 removed outlier: 4.242A pdb=" N MET C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 140 No H-bonds generated for 'chain 'C' and resid 137 through 140' Processing helix chain 'C' and resid 145 through 151 removed outlier: 5.177A pdb=" N TYR C 149 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 199 removed outlier: 4.390A pdb=" N THR C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Proline residue: C 192 - end of helix removed outlier: 3.720A pdb=" N ALA C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 196 " --> pdb=" O PRO C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.981A pdb=" N PHE C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 237 removed outlier: 4.104A pdb=" N ARG C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE C 233 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.613A pdb=" N LEU C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 289 removed outlier: 3.824A pdb=" N VAL C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 302 through 331 removed outlier: 4.328A pdb=" N VAL C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 350 through 361 removed outlier: 3.921A pdb=" N LEU C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 402 removed outlier: 3.919A pdb=" N PHE C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 418 through 441 removed outlier: 3.557A pdb=" N LEU C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 428 " --> pdb=" O TYR C 424 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP C 430 " --> pdb=" O GLY C 426 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'D' and resid 34 through 43 removed outlier: 3.518A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.649A pdb=" N LEU D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 116 No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 132 through 135 No H-bonds generated for 'chain 'D' and resid 132 through 135' Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.578A pdb=" N TYR E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.501A pdb=" N LEU E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 185 removed outlier: 3.680A pdb=" N ALA E 177 " --> pdb=" O SER E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 35 removed outlier: 3.587A pdb=" N ALA F 12 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 69 removed outlier: 3.821A pdb=" N PHE F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 47 " --> pdb=" O PHE F 43 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 52 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 94 removed outlier: 4.308A pdb=" N THR F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Proline residue: F 90 - end of helix Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.564A pdb=" N GLU F 102 " --> pdb=" O PRO F 98 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 134 through 157 removed outlier: 3.546A pdb=" N LEU F 138 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA F 139 " --> pdb=" O PRO F 135 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 155 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 187 removed outlier: 3.967A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Proline residue: F 181 - end of helix removed outlier: 4.288A pdb=" N VAL F 184 " --> pdb=" O GLY F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 197 No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 210 through 235 removed outlier: 3.880A pdb=" N TYR F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 265 removed outlier: 3.600A pdb=" N HIS F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 removed outlier: 3.520A pdb=" N ILE F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 293 through 302 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 325 through 342 removed outlier: 3.895A pdb=" N TYR F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 358 through 377 removed outlier: 3.586A pdb=" N LEU F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 394 Processing sheet with id= A, first strand: chain 'B' and resid 106 through 109 removed outlier: 3.765A pdb=" N LYS B 131 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 224 through 226 removed outlier: 7.152A pdb=" N TYR B 225 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL B 198 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 426 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU B 199 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 428 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B 453 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N MET B 429 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET B 455 " --> pdb=" O MET B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 248 through 251 Processing sheet with id= D, first strand: chain 'B' and resid 258 through 262 Processing sheet with id= E, first strand: chain 'B' and resid 482 through 485 Processing sheet with id= F, first strand: chain 'B' and resid 581 through 585 Processing sheet with id= G, first strand: chain 'B' and resid 617 through 619 Processing sheet with id= H, first strand: chain 'B' and resid 957 through 961 Processing sheet with id= I, first strand: chain 'B' and resid 802 through 805 Processing sheet with id= J, first strand: chain 'B' and resid 841 through 843 Processing sheet with id= K, first strand: chain 'B' and resid 871 through 873 Processing sheet with id= L, first strand: chain 'D' and resid 24 through 27 526 hydrogen bonds defined for protein. 1542 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: 5.95 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.79: 19221 1.79 - 2.40: 150 2.40 - 3.01: 0 3.01 - 3.61: 0 3.61 - 4.22: 3 Bond restraints: 19374 Sorted by residual: bond pdb=" S1 F3S B1106 " pdb="FE4 F3S B1106 " ideal model delta sigma weight residual 2.258 4.221 -1.963 2.00e-02 2.50e+03 9.64e+03 bond pdb=" S4 F3S B1106 " pdb="FE1 F3S B1106 " ideal model delta sigma weight residual 2.233 4.176 -1.943 2.00e-02 2.50e+03 9.44e+03 bond pdb=" S2 F3S B1106 " pdb="FE3 F3S B1106 " ideal model delta sigma weight residual 2.300 4.183 -1.883 2.00e-02 2.50e+03 8.86e+03 bond pdb=" S2 F3S B1106 " pdb="FE4 F3S B1106 " ideal model delta sigma weight residual 2.317 2.197 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" S3 F3S B1106 " pdb="FE1 F3S B1106 " ideal model delta sigma weight residual 2.296 2.188 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 19369 not shown) Histogram of bond angle deviations from ideal: 41.13 - 68.83: 6 68.83 - 96.53: 69 96.53 - 124.23: 25543 124.23 - 151.93: 892 151.93 - 179.63: 12 Bond angle restraints: 26522 Sorted by residual: angle pdb=" S1 F3S B1106 " pdb="FE4 F3S B1106 " pdb=" S3 F3S B1106 " ideal model delta sigma weight residual 114.75 41.13 73.62 3.00e+00 1.11e-01 6.02e+02 angle pdb=" S3 F3S B1106 " pdb="FE1 F3S B1106 " pdb=" S4 F3S B1106 " ideal model delta sigma weight residual 112.59 42.16 70.43 3.00e+00 1.11e-01 5.51e+02 angle pdb=" S1 F3S B1106 " pdb="FE3 F3S B1106 " pdb=" S4 F3S B1106 " ideal model delta sigma weight residual 112.54 144.68 -32.14 3.00e+00 1.11e-01 1.15e+02 angle pdb="FE1 F3S B1106 " pdb=" S4 F3S B1106 " pdb="FE3 F3S B1106 " ideal model delta sigma weight residual 74.86 44.80 30.06 3.00e+00 1.11e-01 1.00e+02 angle pdb=" S2 F3S B1106 " pdb="FE3 F3S B1106 " pdb=" S4 F3S B1106 " ideal model delta sigma weight residual 103.26 73.73 29.53 3.00e+00 1.11e-01 9.69e+01 ... (remaining 26517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 9767 17.48 - 34.96: 1120 34.96 - 52.45: 170 52.45 - 69.93: 40 69.93 - 87.41: 30 Dihedral angle restraints: 11127 sinusoidal: 4407 harmonic: 6720 Sorted by residual: dihedral pdb=" C2B HEC B1101 " pdb=" C3B HEC B1101 " pdb=" CAB HEC B1101 " pdb=" CBB HEC B1101 " ideal model delta sinusoidal sigma weight residual 60.00 146.61 -86.61 2 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" C2B HEC A 302 " pdb=" C3B HEC A 302 " pdb=" CAB HEC A 302 " pdb=" CBB HEC A 302 " ideal model delta sinusoidal sigma weight residual 240.00 173.90 66.10 2 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA CYS A 224 " pdb=" C CYS A 224 " pdb=" N HIS A 225 " pdb=" CA HIS A 225 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 11124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.961: 2855 2.961 - 5.922: 0 5.922 - 8.883: 0 8.883 - 11.844: 0 11.844 - 14.804: 1 Chirality restraints: 2856 Sorted by residual: chirality pdb=" S2 F3S B1106 " pdb="FE1 F3S B1106 " pdb="FE3 F3S B1106 " pdb="FE4 F3S B1106 " both_signs ideal model delta sigma weight residual False 10.77 -4.04 14.80 2.00e-01 2.50e+01 5.48e+03 chirality pdb=" CA ASN E 132 " pdb=" N ASN E 132 " pdb=" C ASN E 132 " pdb=" CB ASN E 132 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ARG B 871 " pdb=" N ARG B 871 " pdb=" C ARG B 871 " pdb=" CB ARG B 871 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2853 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 202 " 0.013 2.00e-02 2.50e+03 6.57e-02 9.70e+01 pdb=" C2C HEC E 202 " -0.179 2.00e-02 2.50e+03 pdb=" C3C HEC E 202 " 0.022 2.00e-02 2.50e+03 pdb=" C4C HEC E 202 " 0.008 2.00e-02 2.50e+03 pdb=" CAC HEC E 202 " 0.027 2.00e-02 2.50e+03 pdb=" CHC HEC E 202 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEC E 202 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC E 202 " 0.065 2.00e-02 2.50e+03 pdb=" NC HEC E 202 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 302 " -0.025 2.00e-02 2.50e+03 6.28e-02 8.87e+01 pdb=" C2C HEC A 302 " 0.172 2.00e-02 2.50e+03 pdb=" C3C HEC A 302 " -0.017 2.00e-02 2.50e+03 pdb=" C4C HEC A 302 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC A 302 " -0.036 2.00e-02 2.50e+03 pdb=" CHC HEC A 302 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC A 302 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEC A 302 " -0.053 2.00e-02 2.50e+03 pdb=" NC HEC A 302 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " 0.021 2.00e-02 2.50e+03 4.81e-02 5.21e+01 pdb=" C2C HEC A 303 " -0.130 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " 0.012 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " 0.039 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.027 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " 0.006 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 280 2.62 - 3.19: 15667 3.19 - 3.76: 32212 3.76 - 4.33: 46503 4.33 - 4.90: 73717 Nonbonded interactions: 168379 Sorted by model distance: nonbonded pdb=" NE2 HIS A 63 " pdb="FE HEC A 304 " model vdw 2.045 3.080 nonbonded pdb=" NE2 HIS A 66 " pdb="FE HEC A 301 " model vdw 2.073 3.080 nonbonded pdb=" NE2 HIS A 140 " pdb="FE HEC B1101 " model vdw 2.115 3.080 nonbonded pdb=" O THR B 859 " pdb=" OG1 THR B 859 " model vdw 2.184 2.440 nonbonded pdb=" S3 F3S B1106 " pdb="FE3 F3S B1106 " model vdw 2.187 2.688 ... (remaining 168374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.760 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 55.850 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.025 1.963 19374 Z= 1.716 Angle : 1.334 73.619 26522 Z= 0.618 Chirality : 0.283 14.804 2856 Planarity : 0.008 0.093 3339 Dihedral : 15.534 87.409 6821 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.42 % Allowed : 8.37 % Favored : 91.22 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.59 (0.13), residues: 2317 helix: -4.56 (0.07), residues: 1049 sheet: -3.09 (0.37), residues: 153 loop : -2.83 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 186 HIS 0.007 0.002 HIS A 127 PHE 0.028 0.002 PHE C 266 TYR 0.026 0.002 TYR E 163 ARG 0.007 0.001 ARG B 990 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 436 time to evaluate : 2.122 Fit side-chains REVERT: A 13 ARG cc_start: 0.7598 (tpt90) cc_final: 0.7036 (tpp80) REVERT: B 126 GLU cc_start: 0.7288 (mp0) cc_final: 0.7078 (mp0) REVERT: B 192 GLN cc_start: 0.6941 (mp10) cc_final: 0.6162 (mp10) REVERT: B 313 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8377 (ptm-80) REVERT: B 694 VAL cc_start: 0.8333 (m) cc_final: 0.8005 (t) REVERT: B 795 LEU cc_start: 0.8563 (mt) cc_final: 0.8031 (mt) REVERT: B 844 ASP cc_start: 0.7775 (m-30) cc_final: 0.7558 (m-30) REVERT: B 968 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.7260 (ttt180) REVERT: C 47 TRP cc_start: 0.7448 (t60) cc_final: 0.7065 (t60) REVERT: C 79 ASN cc_start: 0.8320 (m-40) cc_final: 0.7993 (m110) REVERT: C 207 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7526 (ttmm) REVERT: C 284 LEU cc_start: 0.8591 (tt) cc_final: 0.8348 (tt) REVERT: C 311 MET cc_start: 0.8704 (ttp) cc_final: 0.8489 (ttp) REVERT: E 146 MET cc_start: 0.8403 (ttm) cc_final: 0.8165 (ttm) REVERT: E 153 ASP cc_start: 0.7956 (t70) cc_final: 0.7578 (t0) REVERT: E 157 ASN cc_start: 0.8111 (m110) cc_final: 0.7889 (m-40) REVERT: E 167 TYR cc_start: 0.8484 (p90) cc_final: 0.7995 (p90) REVERT: F 9 LEU cc_start: 0.8410 (tp) cc_final: 0.8205 (tp) REVERT: F 234 LYS cc_start: 0.8281 (tppp) cc_final: 0.8076 (tttp) REVERT: F 319 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7988 (mtt-85) REVERT: F 343 ILE cc_start: 0.8723 (mm) cc_final: 0.8406 (mm) outliers start: 8 outliers final: 4 residues processed: 443 average time/residue: 0.3379 time to fit residues: 220.5489 Evaluate side-chains 330 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 326 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 0.0040 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 56 GLN A 87 ASN A 190 ASN A 199 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 373 GLN B 378 HIS B 456 HIS B 471 HIS B 561 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS B 879 GLN B 955 GLN B 975 GLN C 79 ASN C 141 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 262 HIS C 387 ASN D 174 GLN D 192 ASN E 117 HIS ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS F 304 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 19374 Z= 0.322 Angle : 0.985 55.722 26522 Z= 0.411 Chirality : 0.049 1.219 2856 Planarity : 0.006 0.076 3339 Dihedral : 9.136 88.175 2657 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.87 % Allowed : 12.84 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.15), residues: 2317 helix: -2.99 (0.12), residues: 1084 sheet: -2.95 (0.39), residues: 142 loop : -2.30 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 186 HIS 0.003 0.001 HIS A 63 PHE 0.019 0.001 PHE F 136 TYR 0.023 0.001 TYR F 109 ARG 0.007 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 369 time to evaluate : 2.128 Fit side-chains REVERT: A 13 ARG cc_start: 0.7635 (tpt90) cc_final: 0.7038 (tpp80) REVERT: B 87 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6487 (mt-10) REVERT: B 313 ARG cc_start: 0.8750 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: B 597 ASN cc_start: 0.9000 (t0) cc_final: 0.8548 (t0) REVERT: B 721 LYS cc_start: 0.7007 (mmmt) cc_final: 0.6804 (mmmt) REVERT: B 920 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8759 (m-10) REVERT: B 968 ARG cc_start: 0.7594 (mtp-110) cc_final: 0.7358 (ttt180) REVERT: C 79 ASN cc_start: 0.8296 (m110) cc_final: 0.7943 (m110) REVERT: C 113 GLN cc_start: 0.8068 (mt0) cc_final: 0.7801 (mt0) REVERT: C 207 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7699 (ttmm) REVERT: C 284 LEU cc_start: 0.8674 (tt) cc_final: 0.8431 (tt) REVERT: C 311 MET cc_start: 0.8700 (ttp) cc_final: 0.8461 (ttp) REVERT: C 370 LYS cc_start: 0.8302 (tttp) cc_final: 0.8032 (mttp) REVERT: E 39 ASP cc_start: 0.7395 (m-30) cc_final: 0.6894 (m-30) REVERT: E 110 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7569 (mtm-85) REVERT: E 151 TYR cc_start: 0.8313 (m-80) cc_final: 0.8104 (m-80) REVERT: E 157 ASN cc_start: 0.8265 (m110) cc_final: 0.8036 (m-40) REVERT: E 167 TYR cc_start: 0.8574 (p90) cc_final: 0.7646 (p90) REVERT: F 234 LYS cc_start: 0.8240 (tppp) cc_final: 0.8032 (ttmm) REVERT: F 343 ILE cc_start: 0.8661 (mm) cc_final: 0.8416 (mm) outliers start: 36 outliers final: 25 residues processed: 392 average time/residue: 0.3216 time to fit residues: 188.9723 Evaluate side-chains 353 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 327 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 GLN B 800 HIS B 854 ASN B 936 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 44 HIS F 353 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 19374 Z= 0.305 Angle : 0.881 82.486 26522 Z= 0.374 Chirality : 0.052 1.506 2856 Planarity : 0.005 0.074 3339 Dihedral : 8.761 87.882 2657 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.70 % Allowed : 14.81 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.16), residues: 2317 helix: -2.05 (0.14), residues: 1081 sheet: -2.92 (0.39), residues: 143 loop : -2.04 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 186 HIS 0.003 0.001 HIS E 181 PHE 0.015 0.001 PHE F 167 TYR 0.018 0.001 TYR C 269 ARG 0.007 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 328 time to evaluate : 2.211 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7730 (p) REVERT: B 87 GLU cc_start: 0.7216 (mt-10) cc_final: 0.5997 (mt-10) REVERT: B 597 ASN cc_start: 0.9033 (t0) cc_final: 0.8766 (t0) REVERT: B 843 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8442 (m90) REVERT: B 968 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7277 (ttt180) REVERT: C 79 ASN cc_start: 0.8374 (m110) cc_final: 0.7967 (m-40) REVERT: C 113 GLN cc_start: 0.8254 (mt0) cc_final: 0.7967 (mt0) REVERT: C 207 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7596 (ttmm) REVERT: C 284 LEU cc_start: 0.8706 (tt) cc_final: 0.8456 (tt) REVERT: C 311 MET cc_start: 0.8733 (ttp) cc_final: 0.8468 (ttp) REVERT: C 370 LYS cc_start: 0.8332 (tttp) cc_final: 0.8059 (mttp) REVERT: D 147 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8270 (p0) REVERT: E 39 ASP cc_start: 0.7415 (m-30) cc_final: 0.6645 (m-30) REVERT: E 117 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8342 (m90) REVERT: E 151 TYR cc_start: 0.8435 (m-80) cc_final: 0.8116 (m-80) REVERT: E 157 ASN cc_start: 0.8313 (m110) cc_final: 0.7980 (m-40) REVERT: E 167 TYR cc_start: 0.8596 (p90) cc_final: 0.7733 (p90) REVERT: F 131 TYR cc_start: 0.8807 (t80) cc_final: 0.8606 (t80) outliers start: 52 outliers final: 36 residues processed: 361 average time/residue: 0.3119 time to fit residues: 172.4978 Evaluate side-chains 349 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 309 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 221 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 ASN B 800 HIS B 936 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 19374 Z= 0.229 Angle : 0.846 83.708 26522 Z= 0.355 Chirality : 0.051 1.463 2856 Planarity : 0.005 0.069 3339 Dihedral : 8.506 89.371 2657 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.01 % Allowed : 15.44 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.17), residues: 2317 helix: -1.50 (0.15), residues: 1078 sheet: -2.84 (0.39), residues: 140 loop : -1.85 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 186 HIS 0.004 0.001 HIS F 353 PHE 0.014 0.001 PHE C 323 TYR 0.014 0.001 TYR C 269 ARG 0.007 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 335 time to evaluate : 2.290 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7720 (p) REVERT: B 87 GLU cc_start: 0.7174 (mt-10) cc_final: 0.5927 (mt-10) REVERT: B 158 ASP cc_start: 0.8253 (t0) cc_final: 0.7707 (t0) REVERT: B 597 ASN cc_start: 0.9025 (t0) cc_final: 0.8668 (t0) REVERT: B 843 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8413 (m90) REVERT: B 920 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8775 (m-10) REVERT: B 968 ARG cc_start: 0.7579 (mtp-110) cc_final: 0.7278 (ttt180) REVERT: C 79 ASN cc_start: 0.8113 (m110) cc_final: 0.7754 (m-40) REVERT: C 113 GLN cc_start: 0.8165 (mt0) cc_final: 0.7948 (mt0) REVERT: C 207 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7492 (ttmm) REVERT: C 239 THR cc_start: 0.8574 (t) cc_final: 0.8325 (m) REVERT: C 284 LEU cc_start: 0.8692 (tt) cc_final: 0.8434 (tt) REVERT: C 311 MET cc_start: 0.8735 (ttp) cc_final: 0.8382 (ttp) REVERT: C 370 LYS cc_start: 0.8299 (tttp) cc_final: 0.8032 (mttp) REVERT: E 117 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8213 (m90) REVERT: E 151 TYR cc_start: 0.8430 (m-80) cc_final: 0.8013 (m-80) REVERT: E 157 ASN cc_start: 0.8263 (m110) cc_final: 0.7908 (m-40) REVERT: E 167 TYR cc_start: 0.8490 (p90) cc_final: 0.7629 (p90) REVERT: F 133 ASN cc_start: 0.8955 (p0) cc_final: 0.8402 (p0) REVERT: F 343 ILE cc_start: 0.8634 (mm) cc_final: 0.8394 (mm) outliers start: 58 outliers final: 40 residues processed: 373 average time/residue: 0.3066 time to fit residues: 175.3133 Evaluate side-chains 359 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 315 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 0.0670 chunk 125 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 153 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 19374 Z= 0.207 Angle : 0.823 83.520 26522 Z= 0.343 Chirality : 0.050 1.469 2856 Planarity : 0.004 0.066 3339 Dihedral : 8.208 87.727 2657 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.96 % Allowed : 16.06 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.17), residues: 2317 helix: -1.09 (0.15), residues: 1080 sheet: -2.66 (0.36), residues: 168 loop : -1.73 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 186 HIS 0.005 0.001 HIS C 246 PHE 0.011 0.001 PHE F 167 TYR 0.014 0.001 TYR C 227 ARG 0.007 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 354 time to evaluate : 2.122 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7765 (tpt-90) cc_final: 0.7122 (tpp80) REVERT: A 171 CYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7765 (p) REVERT: B 87 GLU cc_start: 0.7148 (mt-10) cc_final: 0.5884 (mt-10) REVERT: B 158 ASP cc_start: 0.8159 (t0) cc_final: 0.7635 (t0) REVERT: B 276 MET cc_start: 0.8731 (mmm) cc_final: 0.8268 (mtp) REVERT: B 597 ASN cc_start: 0.9042 (t0) cc_final: 0.8701 (t0) REVERT: B 920 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8805 (m-10) REVERT: B 968 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7307 (ttt180) REVERT: C 79 ASN cc_start: 0.7949 (m110) cc_final: 0.7594 (m-40) REVERT: C 186 TRP cc_start: 0.8108 (t60) cc_final: 0.7887 (t60) REVERT: C 193 ASP cc_start: 0.7563 (t70) cc_final: 0.7331 (t0) REVERT: C 207 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7447 (ttmm) REVERT: C 370 LYS cc_start: 0.8278 (tttp) cc_final: 0.7994 (mttp) REVERT: D 34 LEU cc_start: 0.7798 (pp) cc_final: 0.7369 (tt) REVERT: D 49 GLU cc_start: 0.7535 (mp0) cc_final: 0.6800 (mm-30) REVERT: D 147 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8221 (p0) REVERT: E 96 ARG cc_start: 0.7245 (mmt90) cc_final: 0.6965 (mmt-90) REVERT: E 117 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.7876 (m90) REVERT: E 151 TYR cc_start: 0.8438 (m-80) cc_final: 0.8091 (m-80) REVERT: E 167 TYR cc_start: 0.8496 (p90) cc_final: 0.7663 (p90) REVERT: F 9 LEU cc_start: 0.8541 (tp) cc_final: 0.8247 (tp) REVERT: F 133 ASN cc_start: 0.8914 (p0) cc_final: 0.8364 (p0) REVERT: F 318 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8435 (ttpt) REVERT: F 332 TYR cc_start: 0.7999 (m-10) cc_final: 0.7273 (m-80) REVERT: F 343 ILE cc_start: 0.8558 (mm) cc_final: 0.8314 (mm) outliers start: 57 outliers final: 35 residues processed: 393 average time/residue: 0.3126 time to fit residues: 188.7654 Evaluate side-chains 378 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 339 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN F 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 19374 Z= 0.234 Angle : 0.831 83.560 26522 Z= 0.347 Chirality : 0.051 1.480 2856 Planarity : 0.004 0.066 3339 Dihedral : 8.121 87.817 2657 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.12 % Allowed : 16.01 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2317 helix: -0.87 (0.16), residues: 1084 sheet: -2.66 (0.37), residues: 161 loop : -1.68 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 186 HIS 0.009 0.001 HIS F 353 PHE 0.012 0.001 PHE F 223 TYR 0.015 0.001 TYR C 269 ARG 0.008 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 348 time to evaluate : 2.251 Fit side-chains revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (p) REVERT: B 87 GLU cc_start: 0.7183 (mt-10) cc_final: 0.5894 (mt-10) REVERT: B 158 ASP cc_start: 0.8193 (t0) cc_final: 0.7641 (t0) REVERT: B 276 MET cc_start: 0.8746 (mmm) cc_final: 0.8261 (mtp) REVERT: B 597 ASN cc_start: 0.9036 (t0) cc_final: 0.8704 (t0) REVERT: B 795 LEU cc_start: 0.8414 (mt) cc_final: 0.7943 (mt) REVERT: B 920 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8798 (m-10) REVERT: B 968 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7327 (ttt180) REVERT: C 14 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6768 (tpt) REVERT: C 79 ASN cc_start: 0.8048 (m110) cc_final: 0.7740 (m-40) REVERT: C 193 ASP cc_start: 0.7515 (t70) cc_final: 0.7266 (t0) REVERT: C 207 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7412 (ttmm) REVERT: C 370 LYS cc_start: 0.8292 (tttp) cc_final: 0.7983 (mttp) REVERT: C 424 TYR cc_start: 0.8261 (t80) cc_final: 0.7518 (t80) REVERT: D 34 LEU cc_start: 0.7806 (pp) cc_final: 0.7484 (tt) REVERT: D 49 GLU cc_start: 0.7542 (mp0) cc_final: 0.6831 (mm-30) REVERT: D 147 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8190 (p0) REVERT: E 96 ARG cc_start: 0.7253 (mmt90) cc_final: 0.6975 (mmt-90) REVERT: E 117 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.7934 (m90) REVERT: E 167 TYR cc_start: 0.8507 (p90) cc_final: 0.7674 (p90) REVERT: F 9 LEU cc_start: 0.8544 (tp) cc_final: 0.8240 (tp) REVERT: F 133 ASN cc_start: 0.8862 (p0) cc_final: 0.8300 (p0) REVERT: F 332 TYR cc_start: 0.8033 (m-10) cc_final: 0.7257 (m-80) REVERT: F 343 ILE cc_start: 0.8526 (mm) cc_final: 0.8301 (mm) outliers start: 60 outliers final: 44 residues processed: 385 average time/residue: 0.3086 time to fit residues: 182.2961 Evaluate side-chains 376 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 327 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain B residue 931 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 4.9990 chunk 24 optimal weight: 0.0170 chunk 126 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 101 optimal weight: 0.2980 overall best weight: 2.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 19374 Z= 0.299 Angle : 0.858 83.599 26522 Z= 0.360 Chirality : 0.052 1.491 2856 Planarity : 0.004 0.068 3339 Dihedral : 8.174 89.668 2657 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.22 % Allowed : 16.89 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.17), residues: 2317 helix: -0.82 (0.16), residues: 1086 sheet: -2.60 (0.39), residues: 151 loop : -1.66 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 53 HIS 0.004 0.001 HIS C 246 PHE 0.014 0.001 PHE F 223 TYR 0.019 0.001 TYR C 269 ARG 0.009 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 321 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7227 (mt-10) cc_final: 0.5946 (mt-10) REVERT: B 158 ASP cc_start: 0.8150 (t0) cc_final: 0.7703 (t0) REVERT: B 597 ASN cc_start: 0.9048 (t0) cc_final: 0.8759 (t0) REVERT: B 795 LEU cc_start: 0.8548 (mt) cc_final: 0.8074 (mt) REVERT: B 843 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8302 (m90) REVERT: B 918 CYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8058 (t) REVERT: B 968 ARG cc_start: 0.7610 (mtp-110) cc_final: 0.7337 (ttt180) REVERT: C 14 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6809 (tpt) REVERT: C 79 ASN cc_start: 0.8296 (m110) cc_final: 0.8006 (m-40) REVERT: C 193 ASP cc_start: 0.7534 (t70) cc_final: 0.7312 (t0) REVERT: C 207 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7465 (ttmm) REVERT: C 370 LYS cc_start: 0.8338 (tttp) cc_final: 0.8013 (mttp) REVERT: C 424 TYR cc_start: 0.8317 (t80) cc_final: 0.7542 (t80) REVERT: D 34 LEU cc_start: 0.7838 (pp) cc_final: 0.7477 (tt) REVERT: D 147 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8155 (p0) REVERT: E 96 ARG cc_start: 0.7321 (mmt90) cc_final: 0.7031 (mmt-90) REVERT: E 117 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8287 (m90) REVERT: E 167 TYR cc_start: 0.8551 (p90) cc_final: 0.7737 (p90) REVERT: F 9 LEU cc_start: 0.8558 (tp) cc_final: 0.8273 (tp) REVERT: F 133 ASN cc_start: 0.8886 (p0) cc_final: 0.8289 (p0) REVERT: F 300 MET cc_start: 0.8259 (mmp) cc_final: 0.8027 (mmp) REVERT: F 332 TYR cc_start: 0.8204 (m-10) cc_final: 0.7302 (m-80) outliers start: 62 outliers final: 49 residues processed: 362 average time/residue: 0.3291 time to fit residues: 183.9383 Evaluate side-chains 375 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 321 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 931 GLN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 0.6980 chunk 88 optimal weight: 0.0010 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 0.0000 chunk 43 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 0.3168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 19374 Z= 0.191 Angle : 0.821 83.047 26522 Z= 0.339 Chirality : 0.050 1.494 2856 Planarity : 0.004 0.064 3339 Dihedral : 7.804 89.046 2657 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.39 % Allowed : 18.19 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 2317 helix: -0.44 (0.16), residues: 1074 sheet: -2.45 (0.37), residues: 171 loop : -1.60 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 53 HIS 0.005 0.001 HIS C 246 PHE 0.012 0.001 PHE C 209 TYR 0.035 0.001 TYR F 109 ARG 0.007 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 366 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7676 (tpt-90) cc_final: 0.7077 (tpp80) REVERT: B 87 GLU cc_start: 0.7016 (mt-10) cc_final: 0.5741 (mt-10) REVERT: B 158 ASP cc_start: 0.8143 (t0) cc_final: 0.7550 (t0) REVERT: B 597 ASN cc_start: 0.9039 (t0) cc_final: 0.8680 (t0) REVERT: B 920 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8712 (m-10) REVERT: C 14 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6812 (tpt) REVERT: C 79 ASN cc_start: 0.7873 (m110) cc_final: 0.7554 (m-40) REVERT: C 207 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7432 (ttmm) REVERT: C 370 LYS cc_start: 0.8241 (tttp) cc_final: 0.7904 (mttp) REVERT: C 424 TYR cc_start: 0.8203 (t80) cc_final: 0.7498 (t80) REVERT: D 49 GLU cc_start: 0.7189 (mp0) cc_final: 0.6757 (mm-30) REVERT: E 37 MET cc_start: 0.9122 (mtm) cc_final: 0.8910 (mtm) REVERT: E 96 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6887 (mmt-90) REVERT: E 117 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7774 (m90) REVERT: E 167 TYR cc_start: 0.8432 (p90) cc_final: 0.7654 (p90) REVERT: F 28 MET cc_start: 0.6301 (tpt) cc_final: 0.5960 (tpt) REVERT: F 96 PHE cc_start: 0.8195 (t80) cc_final: 0.7958 (t80) REVERT: F 133 ASN cc_start: 0.8834 (p0) cc_final: 0.8277 (p0) REVERT: F 332 TYR cc_start: 0.7832 (m-10) cc_final: 0.7189 (m-80) REVERT: F 343 ILE cc_start: 0.8481 (mm) cc_final: 0.8260 (mm) outliers start: 46 outliers final: 31 residues processed: 399 average time/residue: 0.3088 time to fit residues: 188.4352 Evaluate side-chains 371 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 337 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 123 optimal weight: 0.0170 chunk 89 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 19374 Z= 0.298 Angle : 0.868 83.104 26522 Z= 0.364 Chirality : 0.053 1.510 2856 Planarity : 0.004 0.067 3339 Dihedral : 7.967 89.429 2657 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.34 % Allowed : 18.87 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.18), residues: 2317 helix: -0.44 (0.16), residues: 1078 sheet: -2.43 (0.38), residues: 162 loop : -1.60 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 53 HIS 0.006 0.001 HIS B 843 PHE 0.015 0.001 PHE F 223 TYR 0.018 0.001 TYR C 269 ARG 0.009 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 333 time to evaluate : 2.078 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7735 (tpt-90) cc_final: 0.7138 (tpp80) REVERT: B 158 ASP cc_start: 0.8159 (t0) cc_final: 0.7687 (t0) REVERT: B 276 MET cc_start: 0.8660 (mmm) cc_final: 0.8387 (mtp) REVERT: B 597 ASN cc_start: 0.9054 (t0) cc_final: 0.8777 (t0) REVERT: B 694 VAL cc_start: 0.8408 (m) cc_final: 0.7975 (t) REVERT: B 795 LEU cc_start: 0.8568 (mt) cc_final: 0.8108 (mt) REVERT: B 820 MET cc_start: 0.7913 (ttt) cc_final: 0.7700 (ttp) REVERT: C 14 MET cc_start: 0.7179 (tpt) cc_final: 0.6874 (tpt) REVERT: C 79 ASN cc_start: 0.8286 (m110) cc_final: 0.8002 (m-40) REVERT: C 207 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7482 (ttmm) REVERT: C 370 LYS cc_start: 0.8328 (tttp) cc_final: 0.7941 (mttp) REVERT: C 424 TYR cc_start: 0.8317 (t80) cc_final: 0.7544 (t80) REVERT: D 147 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8173 (p0) REVERT: E 96 ARG cc_start: 0.7245 (mmt90) cc_final: 0.6982 (mmt-90) REVERT: E 117 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8227 (m90) REVERT: E 167 TYR cc_start: 0.8539 (p90) cc_final: 0.7763 (p90) REVERT: F 28 MET cc_start: 0.6315 (tpt) cc_final: 0.5959 (tpt) REVERT: F 122 ASP cc_start: 0.6826 (m-30) cc_final: 0.6478 (m-30) REVERT: F 133 ASN cc_start: 0.8917 (p0) cc_final: 0.8325 (p0) REVERT: F 332 TYR cc_start: 0.8145 (m-10) cc_final: 0.7307 (m-80) outliers start: 45 outliers final: 35 residues processed: 366 average time/residue: 0.3063 time to fit residues: 173.2399 Evaluate side-chains 350 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 313 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 103 optimal weight: 0.0030 chunk 151 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 181 optimal weight: 0.0070 chunk 18 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.9410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 19374 Z= 0.215 Angle : 0.838 82.739 26522 Z= 0.348 Chirality : 0.051 1.518 2856 Planarity : 0.004 0.064 3339 Dihedral : 7.715 88.826 2657 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.92 % Allowed : 19.28 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 2317 helix: -0.25 (0.16), residues: 1073 sheet: -2.45 (0.37), residues: 175 loop : -1.54 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 53 HIS 0.006 0.001 HIS B 843 PHE 0.016 0.001 PHE C 173 TYR 0.041 0.001 TYR F 109 ARG 0.008 0.000 ARG C 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 331 time to evaluate : 1.996 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7693 (tpt-90) cc_final: 0.7043 (tpp80) REVERT: B 87 GLU cc_start: 0.7040 (mt-10) cc_final: 0.5765 (mt-10) REVERT: B 158 ASP cc_start: 0.8152 (t0) cc_final: 0.7610 (t0) REVERT: B 276 MET cc_start: 0.8660 (mmm) cc_final: 0.8361 (mtp) REVERT: B 597 ASN cc_start: 0.9014 (t0) cc_final: 0.8703 (t0) REVERT: B 694 VAL cc_start: 0.8285 (m) cc_final: 0.7826 (t) REVERT: B 795 LEU cc_start: 0.8465 (mt) cc_final: 0.8038 (mt) REVERT: C 14 MET cc_start: 0.7238 (tpt) cc_final: 0.6910 (tpt) REVERT: C 79 ASN cc_start: 0.8058 (m110) cc_final: 0.7808 (m-40) REVERT: C 207 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7439 (ttmm) REVERT: C 370 LYS cc_start: 0.8271 (tttp) cc_final: 0.7894 (mttp) REVERT: C 424 TYR cc_start: 0.8244 (t80) cc_final: 0.7487 (t80) REVERT: C 461 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7325 (ttmm) REVERT: E 96 ARG cc_start: 0.7237 (mmt90) cc_final: 0.6977 (mmt-90) REVERT: E 117 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.7830 (m90) REVERT: E 162 MET cc_start: 0.7896 (ttt) cc_final: 0.7592 (ttt) REVERT: E 167 TYR cc_start: 0.8407 (p90) cc_final: 0.7649 (p90) REVERT: F 28 MET cc_start: 0.6324 (tpt) cc_final: 0.6009 (tpt) REVERT: F 41 GLN cc_start: 0.7602 (tp40) cc_final: 0.7366 (tp40) REVERT: F 122 ASP cc_start: 0.6725 (m-30) cc_final: 0.6325 (m-30) REVERT: F 133 ASN cc_start: 0.8890 (p0) cc_final: 0.8311 (p0) REVERT: F 332 TYR cc_start: 0.7959 (m-10) cc_final: 0.7200 (m-80) REVERT: F 343 ILE cc_start: 0.8485 (mm) cc_final: 0.8272 (mm) outliers start: 37 outliers final: 33 residues processed: 358 average time/residue: 0.3138 time to fit residues: 172.4061 Evaluate side-chains 354 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 167 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113779 restraints weight = 24640.520| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.28 r_work: 0.3074 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 19374 Z= 0.236 Angle : 0.843 82.419 26522 Z= 0.352 Chirality : 0.052 1.539 2856 Planarity : 0.004 0.066 3339 Dihedral : 7.642 88.080 2657 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.03 % Allowed : 19.44 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2317 helix: -0.14 (0.16), residues: 1063 sheet: -2.38 (0.37), residues: 175 loop : -1.50 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 53 HIS 0.006 0.001 HIS B 843 PHE 0.025 0.001 PHE C 173 TYR 0.020 0.001 TYR E 89 ARG 0.008 0.000 ARG C 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.21 seconds wall clock time: 83 minutes 3.32 seconds (4983.32 seconds total)