Starting phenix.real_space_refine on Mon Apr 8 10:30:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/04_2024/8j5t_35993_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/04_2024/8j5t_35993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/04_2024/8j5t_35993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/04_2024/8j5t_35993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/04_2024/8j5t_35993_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/04_2024/8j5t_35993_updated.pdb" } resolution = 2.98 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= 0.003 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 8378 2.51 5 N 2359 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 508": "OD1" <-> "OD2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "B ARG 3": "NH1" <-> "NH2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ASP 424": "OD1" <-> "OD2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ARG 433": "NH1" <-> "NH2" Residue "D ASP 446": "OD1" <-> "OD2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D GLU 474": "OE1" <-> "OE2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D ASP 492": "OD1" <-> "OD2" Residue "D GLU 499": "OE1" <-> "OE2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ASP 524": "OD1" <-> "OD2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D ASP 544": "OD1" <-> "OD2" Residue "D GLU 547": "OE1" <-> "OE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D GLU 586": "OE1" <-> "OE2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D ARG 597": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13234 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3947 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 28, 'TRANS': 490} Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2475 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2185 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain: "D" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4555 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 35, 'TRANS': 572} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {' MG': 2, 'ATP': 2, 'SF4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10760 SG CYS D 292 57.075 44.527 16.961 1.00 73.85 S ATOM 10813 SG CYS D 299 62.442 47.997 16.652 1.00 84.80 S ATOM 10713 SG CYS D 286 58.566 48.547 21.699 1.00 77.21 S ATOM 10946 SG CYS D 317 56.814 50.799 15.887 1.00 80.19 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER A 195 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER A 195 " occ=0.47 residue: pdb=" N GLY A 509 " occ=0.48 ... (2 atoms not shown) pdb=" O GLY A 509 " occ=0.48 residue: pdb=" N GLU A 510 " occ=0.48 ... (7 atoms not shown) pdb=" OE2 GLU A 510 " occ=0.48 residue: pdb=" N SER A 511 " occ=0.48 ... (4 atoms not shown) pdb=" OG SER A 511 " occ=0.48 Time building chain proxies: 7.29, per 1000 atoms: 0.55 Number of scatterers: 13234 At special positions: 0 Unit cell: (85.696, 89.856, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 42 16.00 P 6 15.00 Mg 2 11.99 O 2443 8.00 N 2359 7.00 C 8378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 705 " pdb="FE2 SF4 D 705 " - pdb=" SG CYS D 299 " pdb="FE1 SF4 D 705 " - pdb=" SG CYS D 292 " pdb="FE4 SF4 D 705 " - pdb=" SG CYS D 317 " pdb="FE3 SF4 D 705 " - pdb=" SG CYS D 286 " Number of angles added : 12 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 15 sheets defined 43.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.457A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.680A pdb=" N LEU A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.642A pdb=" N LYS A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 443 through 458 removed outlier: 5.034A pdb=" N GLN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 498 through 504 removed outlier: 4.111A pdb=" N THR A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.805A pdb=" N ARG A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.724A pdb=" N GLU A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 30 removed outlier: 4.191A pdb=" N LEU B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 removed outlier: 4.197A pdb=" N SER B 36 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.665A pdb=" N LYS B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.706A pdb=" N HIS B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 122 removed outlier: 5.274A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 183 through 218 removed outlier: 3.735A pdb=" N ILE B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.899A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 257 removed outlier: 4.275A pdb=" N ARG B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 4.706A pdb=" N THR B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.582A pdb=" N ILE B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 290 through 304 removed outlier: 3.681A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 19 through 37 removed outlier: 4.937A pdb=" N LEU C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 109 removed outlier: 3.620A pdb=" N LYS C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.583A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.712A pdb=" N SER C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 188 through 224 removed outlier: 3.553A pdb=" N ILE C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Proline residue: C 198 - end of helix removed outlier: 4.867A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 4.537A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 279 Proline residue: C 257 - end of helix removed outlier: 3.548A pdb=" N GLY C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.784A pdb=" N MET D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 108 through 119 removed outlier: 4.452A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 139 Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.892A pdb=" N ARG D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.794A pdb=" N VAL D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 removed outlier: 4.330A pdb=" N GLN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 removed outlier: 3.542A pdb=" N GLU D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.574A pdb=" N TYR D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 400 through 408 removed outlier: 3.571A pdb=" N LEU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 4.246A pdb=" N ARG D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 466 Proline residue: D 464 - end of helix Processing helix chain 'D' and resid 474 through 485 removed outlier: 3.884A pdb=" N ASP D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 532 through 547 removed outlier: 3.627A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 596 through 602 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 95 removed outlier: 6.312A pdb=" N SER A 289 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU A 93 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A 291 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 95 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 293 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A 262 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.424A pdb=" N THR A 157 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 144 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 155 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A 146 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 153 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 311 through 313 Processing sheet with id= E, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= F, first strand: chain 'A' and resid 341 through 343 Processing sheet with id= G, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.659A pdb=" N SER A 423 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 426 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 465 through 468 removed outlier: 6.959A pdb=" N ILE A 486 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 67 through 69 removed outlier: 5.161A pdb=" N ILE D 27 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 232 through 238 removed outlier: 6.636A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL D 208 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET D 39 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 210 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY D 41 " --> pdb=" O ILE D 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.514A pdb=" N VAL D 350 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE D 380 " --> pdb=" O HIS D 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 577 through 583 removed outlier: 6.823A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN D 441 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP D 524 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 443 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 11 through 14 removed outlier: 7.039A pdb=" N PHE D 14 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR D 22 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.806A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.851A pdb=" N LYS D 363 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ALA D 370 " --> pdb=" O LYS D 363 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 5287 1.39 - 1.61: 8120 1.61 - 1.84: 68 1.84 - 2.06: 0 2.06 - 2.29: 12 Bond restraints: 13487 Sorted by residual: bond pdb=" C4 ATP D 703 " pdb=" C5 ATP D 703 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C5 ATP D 701 " pdb=" C6 ATP D 701 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.30e+01 bond pdb=" C5 ATP D 703 " pdb=" C6 ATP D 703 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 bond pdb=" C ALA A 450 " pdb=" O ALA A 450 " ideal model delta sigma weight residual 1.237 1.167 0.069 1.17e-02 7.31e+03 3.51e+01 ... (remaining 13482 not shown) Histogram of bond angle deviations from ideal: 72.70 - 85.44: 12 85.44 - 98.17: 3 98.17 - 110.90: 5198 110.90 - 123.63: 12675 123.63 - 136.36: 496 Bond angle restraints: 18384 Sorted by residual: angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 703 " pdb=" O3B ATP D 703 " pdb=" PG ATP D 703 " ideal model delta sigma weight residual 139.87 122.89 16.98 1.00e+00 1.00e+00 2.88e+02 angle pdb=" N VAL B 181 " pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 113.71 102.08 11.63 9.50e-01 1.11e+00 1.50e+02 angle pdb=" PA ATP D 703 " pdb=" O3A ATP D 703 " pdb=" PB ATP D 703 " ideal model delta sigma weight residual 136.83 125.12 11.71 1.00e+00 1.00e+00 1.37e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 127.87 8.96 1.00e+00 1.00e+00 8.03e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7042 17.98 - 35.95: 839 35.95 - 53.93: 174 53.93 - 71.90: 31 71.90 - 89.87: 12 Dihedral angle restraints: 8098 sinusoidal: 3152 harmonic: 4946 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLU D 594 " pdb=" C GLU D 594 " pdb=" N TYR D 595 " pdb=" CA TYR D 595 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C ARG A 447 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" CB ARG A 447 " ideal model delta harmonic sigma weight residual -122.60 -110.95 -11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1826 0.071 - 0.141: 307 0.141 - 0.212: 25 0.212 - 0.283: 5 0.283 - 0.353: 3 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA ARG A 447 " pdb=" N ARG A 447 " pdb=" C ARG A 447 " pdb=" CB ARG A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ALA A 443 " pdb=" N ALA A 443 " pdb=" C ALA A 443 " pdb=" CB ALA A 443 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2163 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 123 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG B 123 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG B 123 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN B 124 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 38 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C MET B 38 " 0.055 2.00e-02 2.50e+03 pdb=" O MET B 38 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 39 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 151 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C LEU C 151 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU C 151 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.017 2.00e-02 2.50e+03 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 124 2.58 - 3.16: 11420 3.16 - 3.74: 19905 3.74 - 4.32: 29416 4.32 - 4.90: 48838 Nonbonded interactions: 109703 Sorted by model distance: nonbonded pdb=" OE1 GLN D 96 " pdb="MG MG D 704 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP D 701 " pdb="MG MG D 702 " model vdw 2.061 2.170 nonbonded pdb=" OG SER D 48 " pdb="MG MG D 704 " model vdw 2.066 2.170 nonbonded pdb=" O1G ATP D 703 " pdb="MG MG D 704 " model vdw 2.124 2.170 nonbonded pdb=" O PHE B 254 " pdb=" N GLY B 257 " model vdw 2.208 2.520 ... (remaining 109698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.510 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 40.320 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:12.130 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: 0.8613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 13487 Z= 0.494 Angle : 0.962 17.519 18384 Z= 0.617 Chirality : 0.054 0.353 2166 Planarity : 0.007 0.106 2370 Dihedral : 16.081 89.875 4926 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.65 % Allowed : 1.38 % Favored : 97.96 % Cbeta Deviations : 0.13 % 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: -2.41 (0.19), residues: 1732 helix: -1.22 (0.17), residues: 807 sheet: -1.53 (0.41), residues: 165 loop : -1.93 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 339 HIS 0.013 0.001 HIS C 62 PHE 0.018 0.002 PHE A 440 TYR 0.017 0.002 TYR A 441 ARG 0.013 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 1.512 Fit side-chains REVERT: A 442 ASP cc_start: 0.7813 (t0) cc_final: 0.7335 (t70) REVERT: B 7 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7353 (ttm170) REVERT: D 63 GLN cc_start: 0.8003 (tt0) cc_final: 0.7523 (tm-30) REVERT: D 65 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7545 (ttp80) REVERT: D 360 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6983 (ptp-110) REVERT: D 409 GLU cc_start: 0.7723 (pp20) cc_final: 0.7412 (pp20) outliers start: 9 outliers final: 5 residues processed: 165 average time/residue: 1.1752 time to fit residues: 213.5359 Evaluate side-chains 127 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.3980 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 249 GLN B 39 GLN B 124 GLN B 190 GLN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13487 Z= 0.222 Angle : 0.617 10.912 18384 Z= 0.317 Chirality : 0.043 0.156 2166 Planarity : 0.005 0.061 2370 Dihedral : 8.289 107.290 1985 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.18 % Allowed : 10.76 % Favored : 87.05 % 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: -1.62 (0.20), residues: 1732 helix: -0.36 (0.18), residues: 794 sheet: -1.52 (0.39), residues: 178 loop : -1.66 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 119 HIS 0.008 0.001 HIS C 62 PHE 0.011 0.001 PHE D 86 TYR 0.010 0.001 TYR D 553 ARG 0.007 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.639 Fit side-chains REVERT: B 95 ILE cc_start: 0.8438 (pt) cc_final: 0.8235 (mt) REVERT: B 189 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8904 (mm) REVERT: D 63 GLN cc_start: 0.7959 (tt0) cc_final: 0.7568 (tm-30) REVERT: D 65 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7427 (ttp80) REVERT: D 235 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: D 248 MET cc_start: 0.7601 (tpt) cc_final: 0.6637 (tpt) REVERT: D 269 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8099 (pp) REVERT: D 360 ARG cc_start: 0.7465 (ttp80) cc_final: 0.6971 (ptp-110) REVERT: D 409 GLU cc_start: 0.7651 (pp20) cc_final: 0.7357 (pp20) outliers start: 30 outliers final: 10 residues processed: 160 average time/residue: 1.1257 time to fit residues: 200.6251 Evaluate side-chains 137 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.0020 chunk 155 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 190 GLN B 211 GLN C 211 ASN ** D 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13487 Z= 0.202 Angle : 0.565 9.652 18384 Z= 0.289 Chirality : 0.042 0.143 2166 Planarity : 0.004 0.061 2370 Dihedral : 7.520 83.980 1980 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.40 % Allowed : 14.62 % Favored : 82.98 % 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: -1.21 (0.20), residues: 1732 helix: 0.06 (0.19), residues: 799 sheet: -1.35 (0.40), residues: 178 loop : -1.56 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.006 0.001 HIS C 62 PHE 0.009 0.001 PHE B 223 TYR 0.009 0.001 TYR A 156 ARG 0.004 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.488 Fit side-chains REVERT: B 189 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8929 (mm) REVERT: B 252 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8846 (m) REVERT: D 63 GLN cc_start: 0.7991 (tt0) cc_final: 0.7529 (tm-30) REVERT: D 99 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7131 (tmt) REVERT: D 235 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: D 248 MET cc_start: 0.7614 (tpt) cc_final: 0.6530 (tpt) REVERT: D 269 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8120 (pp) REVERT: D 360 ARG cc_start: 0.7433 (ttp80) cc_final: 0.6952 (ptp-110) REVERT: D 409 GLU cc_start: 0.7605 (pp20) cc_final: 0.7321 (pp20) outliers start: 33 outliers final: 12 residues processed: 156 average time/residue: 1.1241 time to fit residues: 194.5240 Evaluate side-chains 139 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13487 Z= 0.304 Angle : 0.596 9.707 18384 Z= 0.304 Chirality : 0.044 0.152 2166 Planarity : 0.005 0.059 2370 Dihedral : 7.422 87.940 1980 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.35 % Allowed : 15.56 % Favored : 81.09 % 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: -1.17 (0.20), residues: 1732 helix: 0.10 (0.19), residues: 798 sheet: -1.20 (0.40), residues: 179 loop : -1.56 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.005 0.001 HIS C 62 PHE 0.011 0.001 PHE D 555 TYR 0.013 0.001 TYR A 156 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.499 Fit side-chains REVERT: B 38 MET cc_start: 0.8548 (mtt) cc_final: 0.7971 (mtt) REVERT: B 99 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8534 (tp) REVERT: B 252 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8870 (m) REVERT: B 258 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7771 (m) REVERT: D 63 GLN cc_start: 0.7999 (tt0) cc_final: 0.7658 (tm-30) REVERT: D 65 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7305 (ttp80) REVERT: D 235 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: D 248 MET cc_start: 0.7650 (tpt) cc_final: 0.6519 (tpt) REVERT: D 269 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8130 (pp) REVERT: D 360 ARG cc_start: 0.7461 (ttp80) cc_final: 0.6983 (ptp-110) REVERT: D 409 GLU cc_start: 0.7626 (pp20) cc_final: 0.7302 (pp20) outliers start: 46 outliers final: 23 residues processed: 162 average time/residue: 1.0402 time to fit residues: 188.2728 Evaluate side-chains 148 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 123 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 148 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 overall best weight: 1.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 191 HIS C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13487 Z= 0.197 Angle : 0.544 8.990 18384 Z= 0.277 Chirality : 0.041 0.137 2166 Planarity : 0.004 0.056 2370 Dihedral : 6.934 89.218 1980 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.84 % Allowed : 16.58 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1732 helix: 0.30 (0.19), residues: 805 sheet: -1.14 (0.39), residues: 191 loop : -1.48 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.009 0.001 PHE D 555 TYR 0.009 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.606 Fit side-chains REVERT: B 252 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8844 (m) REVERT: D 63 GLN cc_start: 0.8000 (tt0) cc_final: 0.7577 (tm-30) REVERT: D 235 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: D 248 MET cc_start: 0.7630 (tpt) cc_final: 0.6465 (tpt) REVERT: D 269 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8144 (pp) REVERT: D 360 ARG cc_start: 0.7430 (ttp80) cc_final: 0.6962 (ptp-110) REVERT: D 409 GLU cc_start: 0.7604 (pp20) cc_final: 0.7335 (pp20) REVERT: D 452 ASP cc_start: 0.8172 (p0) cc_final: 0.7829 (p0) outliers start: 39 outliers final: 18 residues processed: 171 average time/residue: 1.0410 time to fit residues: 201.1001 Evaluate side-chains 148 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13487 Z= 0.185 Angle : 0.557 10.425 18384 Z= 0.280 Chirality : 0.041 0.136 2166 Planarity : 0.004 0.055 2370 Dihedral : 6.732 88.312 1980 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.91 % Allowed : 18.04 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1732 helix: 0.41 (0.19), residues: 805 sheet: -1.06 (0.39), residues: 191 loop : -1.44 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.010 0.001 PHE D 555 TYR 0.009 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.406 Fit side-chains REVERT: B 252 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8826 (m) REVERT: D 63 GLN cc_start: 0.8009 (tt0) cc_final: 0.7606 (tm-30) REVERT: D 99 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7257 (tmt) REVERT: D 235 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: D 248 MET cc_start: 0.7589 (tpt) cc_final: 0.6396 (tpt) REVERT: D 269 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8121 (pp) REVERT: D 360 ARG cc_start: 0.7403 (ttp80) cc_final: 0.6935 (ptp-110) REVERT: D 409 GLU cc_start: 0.7571 (pp20) cc_final: 0.7294 (pp20) REVERT: D 545 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8659 (tt) outliers start: 40 outliers final: 21 residues processed: 163 average time/residue: 1.0359 time to fit residues: 188.3463 Evaluate side-chains 154 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13487 Z= 0.382 Angle : 0.642 8.940 18384 Z= 0.324 Chirality : 0.045 0.157 2166 Planarity : 0.005 0.055 2370 Dihedral : 7.088 84.847 1980 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.98 % Allowed : 19.13 % Favored : 77.89 % 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: -1.11 (0.20), residues: 1732 helix: 0.16 (0.19), residues: 796 sheet: -1.19 (0.40), residues: 184 loop : -1.55 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.013 0.002 PHE C 177 TYR 0.015 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 1.513 Fit side-chains REVERT: D 63 GLN cc_start: 0.8009 (tt0) cc_final: 0.7644 (tm-30) REVERT: D 235 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: D 248 MET cc_start: 0.7707 (tpt) cc_final: 0.6473 (tpt) REVERT: D 269 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8112 (pp) REVERT: D 360 ARG cc_start: 0.7436 (ttp80) cc_final: 0.6989 (ptp-110) REVERT: D 409 GLU cc_start: 0.7639 (pp20) cc_final: 0.7305 (pp20) REVERT: D 545 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8656 (tt) outliers start: 41 outliers final: 28 residues processed: 165 average time/residue: 1.0397 time to fit residues: 192.0762 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 211 ASN D 506 GLN D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13487 Z= 0.184 Angle : 0.568 9.749 18384 Z= 0.285 Chirality : 0.041 0.201 2166 Planarity : 0.004 0.056 2370 Dihedral : 6.753 81.578 1980 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.76 % Allowed : 20.44 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1732 helix: 0.43 (0.19), residues: 798 sheet: -1.06 (0.39), residues: 191 loop : -1.42 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.010 0.001 PHE D 555 TYR 0.009 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.503 Fit side-chains REVERT: A 222 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: D 63 GLN cc_start: 0.7993 (tt0) cc_final: 0.7581 (tm-30) REVERT: D 235 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: D 248 MET cc_start: 0.7665 (tpt) cc_final: 0.6493 (tpt) REVERT: D 269 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8130 (pp) REVERT: D 360 ARG cc_start: 0.7396 (ttp80) cc_final: 0.6968 (ptp-110) REVERT: D 409 GLU cc_start: 0.7629 (pp20) cc_final: 0.7317 (pp20) REVERT: D 545 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8637 (tt) outliers start: 38 outliers final: 26 residues processed: 163 average time/residue: 1.1028 time to fit residues: 199.8175 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 144 optimal weight: 0.0060 chunk 153 optimal weight: 0.1980 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 ASN D 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13487 Z= 0.220 Angle : 0.577 8.891 18384 Z= 0.290 Chirality : 0.042 0.179 2166 Planarity : 0.004 0.056 2370 Dihedral : 6.694 81.475 1980 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.69 % Allowed : 21.45 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1732 helix: 0.48 (0.19), residues: 801 sheet: -1.09 (0.38), residues: 196 loop : -1.38 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.011 0.001 PHE D 555 TYR 0.010 0.001 TYR A 156 ARG 0.011 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.414 Fit side-chains REVERT: A 222 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: D 63 GLN cc_start: 0.8006 (tt0) cc_final: 0.7581 (tm-30) REVERT: D 248 MET cc_start: 0.7655 (tpt) cc_final: 0.6405 (tpt) REVERT: D 269 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8130 (pp) REVERT: D 360 ARG cc_start: 0.7395 (ttp80) cc_final: 0.6971 (ptp-110) REVERT: D 409 GLU cc_start: 0.7609 (pp20) cc_final: 0.7304 (pp20) REVERT: D 545 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8659 (tt) outliers start: 37 outliers final: 27 residues processed: 163 average time/residue: 1.0704 time to fit residues: 195.1963 Evaluate side-chains 156 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 590 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 211 ASN D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13487 Z= 0.228 Angle : 0.581 9.909 18384 Z= 0.292 Chirality : 0.042 0.173 2166 Planarity : 0.004 0.058 2370 Dihedral : 6.564 81.474 1977 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.55 % Allowed : 21.60 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1732 helix: 0.47 (0.19), residues: 803 sheet: -1.16 (0.38), residues: 195 loop : -1.34 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.011 0.001 PHE D 555 TYR 0.010 0.001 TYR A 156 ARG 0.011 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.689 Fit side-chains REVERT: A 222 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: D 63 GLN cc_start: 0.8003 (tt0) cc_final: 0.7571 (tm-30) REVERT: D 248 MET cc_start: 0.7679 (tpt) cc_final: 0.6445 (tpt) REVERT: D 269 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8132 (pp) REVERT: D 360 ARG cc_start: 0.7392 (ttp80) cc_final: 0.6973 (ptp-110) REVERT: D 409 GLU cc_start: 0.7627 (pp20) cc_final: 0.7311 (pp20) REVERT: D 545 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8658 (tt) outliers start: 35 outliers final: 26 residues processed: 162 average time/residue: 1.0375 time to fit residues: 187.7754 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 119 optimal weight: 5.9990 overall best weight: 0.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 ASN D 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089867 restraints weight = 20360.621| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.08 r_work: 0.2956 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13487 Z= 0.179 Angle : 0.562 9.097 18384 Z= 0.282 Chirality : 0.041 0.161 2166 Planarity : 0.004 0.059 2370 Dihedral : 6.416 79.841 1977 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.69 % Allowed : 21.53 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1732 helix: 0.73 (0.19), residues: 789 sheet: -0.97 (0.39), residues: 189 loop : -1.37 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.010 0.001 PHE D 555 TYR 0.008 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.30 seconds wall clock time: 73 minutes 38.51 seconds (4418.51 seconds total)