Starting phenix.real_space_refine on Sat Jul 4 07:56:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.map" model { file = "/net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w72_32336/07_2026/7w72_32336.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 80 5.16 5 C 12526 2.51 5 N 3167 2.21 5 O 3413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19188 Number of models: 1 Model: "" Number of chains: 10 Chain: "U" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3427 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 400} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4150 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 31, 'TRANS': 501} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4268 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 40, 'TRANS': 486} Chain: "K" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2676 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 19, 'TRANS': 310} Chain breaks: 1 Chain: "A" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4557 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 1 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'8JY': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.59, per 1000 atoms: 0.19 Number of scatterers: 19188 At special positions: 0 Unit cell: (94.64, 120.64, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 80 16.00 P 1 15.00 O 3413 8.00 N 3167 7.00 C 12526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS T 182 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 195 " - pdb=" SG CYS T 272 " distance=2.03 Simple disulfide: pdb=" SG CYS T 226 " - pdb=" SG CYS T 231 " distance=2.05 Simple disulfide: pdb=" SG CYS K 275 " - pdb=" SG CYS K 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 266 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG N 1 " - " ASN A 203 " " NAG S 601 " - " ASN S 267 " " NAG T 601 " - " ASN T 327 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 782.6 milliseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 15 sheets defined 48.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'U' and resid 2 through 22 removed outlier: 4.101A pdb=" N VAL U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU U 7 " --> pdb=" O ALA U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 31 Processing helix chain 'U' and resid 40 through 54 Processing helix chain 'U' and resid 66 through 76 removed outlier: 3.643A pdb=" N PHE U 75 " --> pdb=" O TYR U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 117 removed outlier: 4.049A pdb=" N LEU U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 146 Processing helix chain 'U' and resid 147 through 156 Processing helix chain 'U' and resid 159 through 177 Processing helix chain 'U' and resid 178 through 194 Processing helix chain 'U' and resid 199 through 212 Processing helix chain 'U' and resid 219 through 249 removed outlier: 3.834A pdb=" N LEU U 248 " --> pdb=" O SER U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 252 through 264 removed outlier: 4.447A pdb=" N PHE U 260 " --> pdb=" O ALA U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 280 Processing helix chain 'U' and resid 285 through 300 removed outlier: 4.086A pdb=" N PHE U 289 " --> pdb=" O PHE U 285 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL U 297 " --> pdb=" O PHE U 293 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE U 298 " --> pdb=" O GLN U 294 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR U 300 " --> pdb=" O ASN U 296 " (cutoff:3.500A) Processing helix chain 'U' and resid 300 through 308 Processing helix chain 'U' and resid 311 through 326 Processing helix chain 'U' and resid 331 through 340 removed outlier: 3.838A pdb=" N VAL U 335 " --> pdb=" O THR U 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU U 337 " --> pdb=" O GLY U 333 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR U 338 " --> pdb=" O ASP U 334 " (cutoff:3.500A) Processing helix chain 'U' and resid 341 through 349 removed outlier: 5.026A pdb=" N HIS U 347 " --> pdb=" O VAL U 344 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 378 removed outlier: 3.909A pdb=" N LEU U 358 " --> pdb=" O ASN U 354 " (cutoff:3.500A) Proline residue: U 370 - end of helix Processing helix chain 'U' and resid 383 through 418 removed outlier: 4.038A pdb=" N PHE U 387 " --> pdb=" O ASN U 383 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 30 Processing helix chain 'S' and resid 30 through 40 Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 112 through 119 removed outlier: 3.570A pdb=" N GLU S 116 " --> pdb=" O LEU S 112 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 130 Processing helix chain 'S' and resid 179 through 194 Processing helix chain 'S' and resid 198 through 205 removed outlier: 4.252A pdb=" N ALA S 202 " --> pdb=" O ASP S 198 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA S 203 " --> pdb=" O VAL S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 247 through 262 removed outlier: 4.512A pdb=" N GLN S 256 " --> pdb=" O ARG S 252 " (cutoff:3.500A) Proline residue: S 257 - end of helix Processing helix chain 'S' and resid 263 through 266 Processing helix chain 'S' and resid 296 through 303 Proline residue: S 301 - end of helix Processing helix chain 'S' and resid 304 through 311 removed outlier: 3.637A pdb=" N ARG S 310 " --> pdb=" O PRO S 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 330 through 334 Processing helix chain 'S' and resid 381 through 397 removed outlier: 3.767A pdb=" N VAL S 388 " --> pdb=" O ARG S 384 " (cutoff:3.500A) Processing helix chain 'S' and resid 419 through 452 Processing helix chain 'S' and resid 458 through 480 removed outlier: 3.726A pdb=" N ALA S 480 " --> pdb=" O ALA S 476 " (cutoff:3.500A) Processing helix chain 'S' and resid 483 through 503 Processing helix chain 'S' and resid 504 through 508 removed outlier: 3.812A pdb=" N LEU S 508 " --> pdb=" O ALA S 505 " (cutoff:3.500A) Processing helix chain 'S' and resid 514 through 519 removed outlier: 3.686A pdb=" N PHE S 519 " --> pdb=" O ASP S 515 " (cutoff:3.500A) Processing helix chain 'S' and resid 522 through 539 Proline residue: S 528 - end of helix removed outlier: 4.298A pdb=" N VAL S 531 " --> pdb=" O LEU S 527 " (cutoff:3.500A) Proline residue: S 532 - end of helix removed outlier: 3.818A pdb=" N LEU S 537 " --> pdb=" O ILE S 533 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS S 539 " --> pdb=" O LEU S 535 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 80 removed outlier: 3.841A pdb=" N LEU T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE T 77 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER T 78 " --> pdb=" O GLY T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 139 Processing helix chain 'T' and resid 141 through 145 Processing helix chain 'T' and resid 182 through 192 Proline residue: T 188 - end of helix Processing helix chain 'T' and resid 199 through 205 removed outlier: 4.059A pdb=" N SER T 202 " --> pdb=" O ALA T 199 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL T 203 " --> pdb=" O GLY T 200 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU T 204 " --> pdb=" O LEU T 201 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU T 205 " --> pdb=" O SER T 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 199 through 205' Processing helix chain 'T' and resid 206 through 211 Processing helix chain 'T' and resid 259 through 265 Processing helix chain 'T' and resid 342 through 346 removed outlier: 3.968A pdb=" N ALA T 346 " --> pdb=" O GLU T 343 " (cutoff:3.500A) Processing helix chain 'T' and resid 452 through 456 removed outlier: 4.027A pdb=" N TYR T 456 " --> pdb=" O TRP T 453 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 463 Processing helix chain 'T' and resid 490 through 494 removed outlier: 3.632A pdb=" N SER T 494 " --> pdb=" O LEU T 491 " (cutoff:3.500A) Processing helix chain 'T' and resid 525 through 548 removed outlier: 3.773A pdb=" N ILE T 529 " --> pdb=" O PRO T 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 76 removed outlier: 3.544A pdb=" N VAL K 62 " --> pdb=" O ASN K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 127 through 137 Processing helix chain 'K' and resid 180 through 193 removed outlier: 3.581A pdb=" N LYS K 193 " --> pdb=" O GLN K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 211 removed outlier: 3.596A pdb=" N SER K 210 " --> pdb=" O GLN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 259 removed outlier: 3.796A pdb=" N GLU K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 271 Processing helix chain 'K' and resid 299 through 303 removed outlier: 3.565A pdb=" N PHE K 303 " --> pdb=" O ILE K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 357 removed outlier: 3.600A pdb=" N HIS K 356 " --> pdb=" O ALA K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 386 Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 84 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 189 through 201 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 248 through 263 removed outlier: 4.076A pdb=" N LEU A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 300 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.751A pdb=" N PHE A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 310' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 331 through 347 Processing helix chain 'A' and resid 370 through 398 Proline residue: A 376 - end of helix removed outlier: 4.329A pdb=" N LEU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.643A pdb=" N ILE A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.521A pdb=" N ARG A 484 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 485 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 517 Processing helix chain 'A' and resid 517 through 534 removed outlier: 3.571A pdb=" N GLY A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Proline residue: A 530 - end of helix removed outlier: 3.607A pdb=" N LEU A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.548A pdb=" N GLN A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 606 through 619 removed outlier: 3.958A pdb=" N CYS A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 86 through 89 Processing sheet with id=AA2, first strand: chain 'S' and resid 86 through 89 Processing sheet with id=AA3, first strand: chain 'S' and resid 267 through 268 removed outlier: 6.436A pdb=" N SER S 272 " --> pdb=" O TYR T 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 267 through 268 removed outlier: 8.125A pdb=" N LEU S 322 " --> pdb=" O GLY S 226 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU S 228 " --> pdb=" O LEU S 322 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE S 324 " --> pdb=" O GLU S 228 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR S 230 " --> pdb=" O PHE S 324 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU S 326 " --> pdb=" O THR S 230 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER S 232 " --> pdb=" O LEU S 326 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY S 358 " --> pdb=" O VAL S 321 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN S 323 " --> pdb=" O GLY S 358 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N MET S 360 " --> pdb=" O ASN S 323 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU S 325 " --> pdb=" O MET S 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 241 through 244 Processing sheet with id=AA6, first strand: chain 'S' and resid 285 through 287 removed outlier: 3.916A pdb=" N SER S 292 " --> pdb=" O ASP S 287 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR S 293 " --> pdb=" O TYR S 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 171 through 176 removed outlier: 6.032A pdb=" N GLY T 109 " --> pdb=" O PHE T 89 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE T 89 " --> pdb=" O GLY T 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU T 111 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU T 87 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP T 113 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU T 85 " --> pdb=" O TRP T 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP T 115 " --> pdb=" O ARG T 83 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR T 215 " --> pdb=" O VAL T 245 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU T 30 " --> pdb=" O SER T 276 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER T 278 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU T 32 " --> pdb=" O SER T 278 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL T 280 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU T 34 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL T 282 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE T 36 " --> pdb=" O VAL T 282 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR T 302 " --> pdb=" O ILE T 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 171 through 176 removed outlier: 6.032A pdb=" N GLY T 109 " --> pdb=" O PHE T 89 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE T 89 " --> pdb=" O GLY T 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU T 111 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU T 87 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP T 113 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU T 85 " --> pdb=" O TRP T 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP T 115 " --> pdb=" O ARG T 83 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N ARG T 83 " --> pdb=" O PRO T 224 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU T 30 " --> pdb=" O SER T 276 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER T 278 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU T 32 " --> pdb=" O SER T 278 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL T 280 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU T 34 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL T 282 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE T 36 " --> pdb=" O VAL T 282 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR T 302 " --> pdb=" O ILE T 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 353 through 359 removed outlier: 3.644A pdb=" N VAL T 442 " --> pdb=" O THR T 370 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N VAL T 439 " --> pdb=" O ILE T 402 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ILE T 402 " --> pdb=" O VAL T 439 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N LYS T 441 " --> pdb=" O LEU T 400 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N LEU T 400 " --> pdb=" O LYS T 441 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N SER T 443 " --> pdb=" O HIS T 398 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N HIS T 398 " --> pdb=" O SER T 443 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN T 445 " --> pdb=" O TYR T 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 413 through 417 removed outlier: 3.873A pdb=" N TYR T 413 " --> pdb=" O LEU T 431 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU T 474 " --> pdb=" O PRO T 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 464 through 466 Processing sheet with id=AB3, first strand: chain 'K' and resid 121 through 122 removed outlier: 7.560A pdb=" N TYR K 121 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU K 84 " --> pdb=" O TYR K 121 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA K 47 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N MET K 85 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 49 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE K 157 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE K 202 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE K 159 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP K 204 " --> pdb=" O ILE K 159 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N MET K 161 " --> pdb=" O ASP K 204 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU K 199 " --> pdb=" O MET K 221 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU K 223 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE K 201 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 165 through 166 removed outlier: 3.756A pdb=" N PHE K 169 " --> pdb=" O GLY K 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 208 through 209 removed outlier: 5.971A pdb=" N SER A 143 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 221 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 315 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 208 through 209 removed outlier: 5.971A pdb=" N SER A 143 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 221 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 315 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 235 " --> pdb=" O THR A 267 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2871 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: 3.68 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5796 1.34 - 1.46: 4260 1.46 - 1.58: 9506 1.58 - 1.70: 7 1.70 - 1.83: 134 Bond restraints: 19703 Sorted by residual: bond pdb=" N PRO T 224 " pdb=" CA PRO T 224 " ideal model delta sigma weight residual 1.472 1.696 -0.224 1.21e-02 6.83e+03 3.43e+02 bond pdb=" C ARG T 223 " pdb=" N PRO T 224 " ideal model delta sigma weight residual 1.333 1.450 -0.117 1.01e-02 9.80e+03 1.33e+02 bond pdb=" O07 8JY U 501 " pdb=" P13 8JY U 501 " ideal model delta sigma weight residual 1.660 1.818 -0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C SER K 217 " pdb=" N PRO K 218 " ideal model delta sigma weight residual 1.334 1.497 -0.163 2.34e-02 1.83e+03 4.85e+01 bond pdb=" O14 8JY U 501 " pdb=" P13 8JY U 501 " ideal model delta sigma weight residual 1.624 1.745 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 19698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 26675 3.95 - 7.90: 149 7.90 - 11.85: 21 11.85 - 15.80: 11 15.80 - 19.75: 6 Bond angle restraints: 26862 Sorted by residual: angle pdb=" C ARG T 223 " pdb=" N PRO T 224 " pdb=" CA PRO T 224 " ideal model delta sigma weight residual 120.23 139.98 -19.75 1.23e+00 6.61e-01 2.58e+02 angle pdb=" C VAL K 228 " pdb=" CA VAL K 228 " pdb=" CB VAL K 228 " ideal model delta sigma weight residual 111.88 130.93 -19.05 1.28e+00 6.10e-01 2.22e+02 angle pdb=" C SER K 217 " pdb=" N PRO K 218 " pdb=" CA PRO K 218 " ideal model delta sigma weight residual 119.84 137.57 -17.73 1.25e+00 6.40e-01 2.01e+02 angle pdb=" N PRO T 224 " pdb=" CA PRO T 224 " pdb=" C PRO T 224 " ideal model delta sigma weight residual 110.50 92.80 17.70 1.57e+00 4.06e-01 1.27e+02 angle pdb=" N LEU T 423 " pdb=" CA LEU T 423 " pdb=" CB LEU T 423 " ideal model delta sigma weight residual 110.98 96.63 14.35 1.32e+00 5.74e-01 1.18e+02 ... (remaining 26857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.29: 10639 20.29 - 40.59: 822 40.59 - 60.88: 128 60.88 - 81.18: 30 81.18 - 101.47: 20 Dihedral angle restraints: 11639 sinusoidal: 4574 harmonic: 7065 Sorted by residual: dihedral pdb=" C VAL K 228 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " pdb=" CB VAL K 228 " ideal model delta harmonic sigma weight residual -122.00 -157.26 35.26 0 2.50e+00 1.60e-01 1.99e+02 dihedral pdb=" N VAL K 228 " pdb=" C VAL K 228 " pdb=" CA VAL K 228 " pdb=" CB VAL K 228 " ideal model delta harmonic sigma weight residual 123.40 151.76 -28.36 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" CB CYS T 226 " pdb=" SG CYS T 226 " pdb=" SG CYS T 231 " pdb=" CB CYS T 231 " ideal model delta sinusoidal sigma weight residual -86.00 -2.40 -83.60 1 1.00e+01 1.00e-02 8.53e+01 ... (remaining 11636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 3077 0.254 - 0.507: 10 0.507 - 0.761: 0 0.761 - 1.015: 0 1.015 - 1.268: 1 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA VAL K 228 " pdb=" N VAL K 228 " pdb=" C VAL K 228 " pdb=" CB VAL K 228 " both_signs ideal model delta sigma weight residual False 2.44 1.17 1.27 2.00e-01 2.50e+01 4.02e+01 chirality pdb=" CA PRO T 224 " pdb=" N PRO T 224 " pdb=" C PRO T 224 " pdb=" CB PRO T 224 " both_signs ideal model delta sigma weight residual False 2.72 3.18 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA GLU T 184 " pdb=" N GLU T 184 " pdb=" C GLU T 184 " pdb=" CB GLU T 184 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 3085 not shown) Planarity restraints: 3363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR U 195 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO U 196 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO U 196 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO U 196 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 245 " -0.028 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP S 245 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP S 245 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP S 245 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP S 245 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP S 245 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 245 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 245 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 245 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP S 245 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 376 " -0.022 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP U 376 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP U 376 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP U 376 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP U 376 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP U 376 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP U 376 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 376 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 376 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP U 376 " -0.003 2.00e-02 2.50e+03 ... (remaining 3360 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 204 2.61 - 3.18: 16680 3.18 - 3.75: 31164 3.75 - 4.33: 44445 4.33 - 4.90: 73183 Nonbonded interactions: 165676 Sorted by model distance: nonbonded pdb=" O ARG A 313 " pdb=" NH2 ARG A 352 " model vdw 2.032 3.120 nonbonded pdb=" O TRP T 391 " pdb=" CE3 TRP T 391 " model vdw 2.090 3.340 nonbonded pdb=" OG SER T 156 " pdb=" OE1 GLU T 429 " model vdw 2.107 3.040 nonbonded pdb=" O ASP K 115 " pdb=" OD1 ASP K 115 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLN A 297 " pdb=" OG SER A 519 " model vdw 2.158 3.040 ... (remaining 165671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.750 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 0.224 19714 Z= 0.376 Angle : 0.916 19.745 26887 Z= 0.539 Chirality : 0.058 1.268 3088 Planarity : 0.005 0.113 3360 Dihedral : 15.156 101.472 7052 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 0.39 % Allowed : 1.25 % Favored : 98.36 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2384 helix: 0.32 (0.16), residues: 1039 sheet: -0.80 (0.27), residues: 389 loop : -1.94 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 71 TYR 0.036 0.002 TYR A 175 PHE 0.035 0.002 PHE U 315 TRP 0.073 0.002 TRP S 245 HIS 0.006 0.001 HIS S 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.36 (19703) covalent geometry : angle 0.91216 / 0.54 (26862) SS BOND : bond 0.00950 / 0.55 ( 5) SS BOND : angle 3.54708 / 1.60 ( 10) hydrogen bonds : bond 0.14876 / 10.31 ( 932) hydrogen bonds : angle 6.79181 / 4.78 ( 2871) Misc. bond : bond 0.16824 / 8.85 ( 1) link_BETA1-4 : bond 0.00260 / 0.13 ( 2) link_BETA1-4 : angle 2.20552 / 1.00 ( 6) link_NAG-ASN : bond 0.00289 / 0.14 ( 3) link_NAG-ASN : angle 2.09251 / 1.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: U 281 MET cc_start: 0.7706 (tpt) cc_final: 0.7317 (tpt) REVERT: S 269 SER cc_start: 0.7748 (t) cc_final: 0.7516 (t) REVERT: S 529 MET cc_start: 0.2020 (ttp) cc_final: 0.1095 (mtt) REVERT: A 439 LEU cc_start: 0.8295 (tt) cc_final: 0.7939 (mt) outliers start: 8 outliers final: 4 residues processed: 301 average time/residue: 0.1301 time to fit residues: 59.9206 Evaluate side-chains 225 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 110 GLN U 296 ASN S 114 HIS ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 424 GLN T 516 ASN K 45 ASN K 107 ASN K 207 GLN A 449 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085753 restraints weight = 28761.382| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.03 r_work: 0.2829 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19714 Z= 0.147 Angle : 0.645 9.645 26887 Z= 0.326 Chirality : 0.043 0.203 3088 Planarity : 0.006 0.112 3360 Dihedral : 6.872 88.980 2648 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.06 % Allowed : 6.71 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2384 helix: 0.78 (0.16), residues: 1053 sheet: -0.86 (0.26), residues: 394 loop : -1.78 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 340 TYR 0.020 0.001 TYR K 59 PHE 0.028 0.001 PHE U 315 TRP 0.029 0.002 TRP S 245 HIS 0.007 0.001 HIS T 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (19703) covalent geometry : angle 0.64344 / 0.33 (26862) SS BOND : bond 0.00406 / 0.26 ( 5) SS BOND : angle 1.29695 / 0.63 ( 10) hydrogen bonds : bond 0.04264 / 2.81 ( 932) hydrogen bonds : angle 5.06161 / 3.56 ( 2871) Misc. bond : bond 0.00207 / 0.11 ( 1) link_BETA1-4 : bond 0.00366 / 0.18 ( 2) link_BETA1-4 : angle 1.83735 / 0.77 ( 6) link_NAG-ASN : bond 0.00294 / 0.14 ( 3) link_NAG-ASN : angle 2.10016 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: U 416 LEU cc_start: 0.8861 (mt) cc_final: 0.8627 (mt) REVERT: S 269 SER cc_start: 0.8118 (t) cc_final: 0.7884 (t) REVERT: T 325 MET cc_start: 0.8219 (tpp) cc_final: 0.7854 (tpp) REVERT: A 439 LEU cc_start: 0.8527 (tt) cc_final: 0.8089 (mt) REVERT: A 460 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6589 (mm-30) REVERT: A 534 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8354 (pp) outliers start: 22 outliers final: 14 residues processed: 267 average time/residue: 0.1185 time to fit residues: 50.8747 Evaluate side-chains 248 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 209 GLN Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 534 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 205 optimal weight: 0.0970 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 545 ASN K 45 ASN K 107 ASN K 173 GLN A 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.082678 restraints weight = 29156.905| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.07 r_work: 0.2773 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19714 Z= 0.219 Angle : 0.655 9.607 26887 Z= 0.330 Chirality : 0.044 0.198 3088 Planarity : 0.005 0.108 3360 Dihedral : 6.552 80.582 2641 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.83 % Allowed : 8.78 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2384 helix: 0.87 (0.16), residues: 1062 sheet: -0.93 (0.25), residues: 388 loop : -1.70 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 71 TYR 0.027 0.002 TYR K 59 PHE 0.020 0.002 PHE U 315 TRP 0.027 0.002 TRP S 245 HIS 0.006 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (19703) covalent geometry : angle 0.65244 / 0.33 (26862) SS BOND : bond 0.00603 / 0.43 ( 5) SS BOND : angle 1.33606 / 0.66 ( 10) hydrogen bonds : bond 0.04275 / 2.80 ( 932) hydrogen bonds : angle 4.84472 / 3.41 ( 2871) Misc. bond : bond 0.00204 / 0.11 ( 1) link_BETA1-4 : bond 0.00297 / 0.14 ( 2) link_BETA1-4 : angle 2.01580 / 0.93 ( 6) link_NAG-ASN : bond 0.00303 / 0.14 ( 3) link_NAG-ASN : angle 2.13038 / 1.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: U 126 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8540 (tt) REVERT: S 119 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6744 (tt) REVERT: S 269 SER cc_start: 0.8125 (t) cc_final: 0.7889 (t) REVERT: S 529 MET cc_start: 0.1189 (tmm) cc_final: -0.0047 (mtt) REVERT: T 277 GLU cc_start: 0.8614 (tt0) cc_final: 0.8295 (tt0) REVERT: K 291 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: A 250 ASP cc_start: 0.8414 (m-30) cc_final: 0.8132 (m-30) REVERT: A 375 MET cc_start: 0.9000 (tpp) cc_final: 0.8672 (mmm) REVERT: A 439 LEU cc_start: 0.8574 (tt) cc_final: 0.8094 (mt) REVERT: A 534 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8393 (pp) outliers start: 38 outliers final: 27 residues processed: 253 average time/residue: 0.1121 time to fit residues: 46.0403 Evaluate side-chains 249 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 209 GLN Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain U residue 381 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain K residue 45 ASN Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 18 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 237 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 409 ASN T 462 HIS T 527 ASN K 45 ASN K 107 ASN A 592 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085034 restraints weight = 28903.954| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.06 r_work: 0.2804 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19714 Z= 0.141 Angle : 0.594 9.103 26887 Z= 0.300 Chirality : 0.042 0.184 3088 Planarity : 0.005 0.106 3360 Dihedral : 6.270 76.255 2641 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.22 % Allowed : 9.50 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2384 helix: 1.07 (0.16), residues: 1064 sheet: -1.00 (0.25), residues: 389 loop : -1.61 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 47 TYR 0.024 0.001 TYR K 59 PHE 0.019 0.001 PHE T 381 TRP 0.018 0.001 TRP S 245 HIS 0.006 0.001 HIS T 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (19703) covalent geometry : angle 0.59208 / 0.30 (26862) SS BOND : bond 0.00410 / 0.29 ( 5) SS BOND : angle 1.09315 / 0.55 ( 10) hydrogen bonds : bond 0.03825 / 2.49 ( 932) hydrogen bonds : angle 4.61401 / 3.25 ( 2871) Misc. bond : bond 0.00190 / 0.10 ( 1) link_BETA1-4 : bond 0.00314 / 0.15 ( 2) link_BETA1-4 : angle 1.66558 / 0.74 ( 6) link_NAG-ASN : bond 0.00291 / 0.14 ( 3) link_NAG-ASN : angle 2.05400 / 1.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 126 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8581 (tt) REVERT: S 72 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7586 (tm-30) REVERT: S 119 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6559 (tt) REVERT: S 179 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: S 269 SER cc_start: 0.8070 (t) cc_final: 0.7844 (t) REVERT: S 529 MET cc_start: 0.1371 (tmm) cc_final: 0.0056 (mtt) REVERT: T 277 GLU cc_start: 0.8608 (tt0) cc_final: 0.8306 (tt0) REVERT: T 325 MET cc_start: 0.8247 (tpp) cc_final: 0.7901 (tpp) REVERT: T 524 MET cc_start: 0.8093 (ttm) cc_final: 0.7777 (mtp) REVERT: T 526 TYR cc_start: 0.8083 (t80) cc_final: 0.7680 (t80) REVERT: K 44 ASN cc_start: 0.8052 (m-40) cc_final: 0.7729 (m-40) REVERT: K 291 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: A 111 LYS cc_start: 0.8394 (tttp) cc_final: 0.8181 (ttmp) REVERT: A 250 ASP cc_start: 0.8361 (m-30) cc_final: 0.8001 (m-30) REVERT: A 375 MET cc_start: 0.8982 (tpp) cc_final: 0.8714 (mmm) REVERT: A 534 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8426 (pp) outliers start: 46 outliers final: 29 residues processed: 280 average time/residue: 0.1233 time to fit residues: 56.0540 Evaluate side-chains 265 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 209 GLN Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 430 MET Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 527 ASN Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 123 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN K 45 ASN K 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.084884 restraints weight = 28904.757| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.07 r_work: 0.2809 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19714 Z= 0.151 Angle : 0.599 9.000 26887 Z= 0.302 Chirality : 0.042 0.188 3088 Planarity : 0.005 0.103 3360 Dihedral : 6.108 72.523 2641 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.27 % Allowed : 10.95 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2384 helix: 1.14 (0.16), residues: 1063 sheet: -0.99 (0.25), residues: 389 loop : -1.56 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 47 TYR 0.025 0.001 TYR K 59 PHE 0.018 0.001 PHE T 381 TRP 0.017 0.001 TRP U 376 HIS 0.006 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (19703) covalent geometry : angle 0.59702 / 0.30 (26862) SS BOND : bond 0.00401 / 0.26 ( 5) SS BOND : angle 1.28983 / 0.70 ( 10) hydrogen bonds : bond 0.03797 / 2.47 ( 932) hydrogen bonds : angle 4.55105 / 3.21 ( 2871) Misc. bond : bond 0.00172 / 0.09 ( 1) link_BETA1-4 : bond 0.00302 / 0.14 ( 2) link_BETA1-4 : angle 1.68523 / 0.76 ( 6) link_NAG-ASN : bond 0.00290 / 0.14 ( 3) link_NAG-ASN : angle 2.03791 / 1.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 72 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7538 (tm-30) REVERT: S 119 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6445 (tt) REVERT: S 206 ASP cc_start: 0.7696 (t0) cc_final: 0.7197 (t0) REVERT: S 269 SER cc_start: 0.8063 (t) cc_final: 0.7821 (t) REVERT: S 529 MET cc_start: 0.1381 (tmm) cc_final: 0.0087 (mtt) REVERT: T 277 GLU cc_start: 0.8629 (tt0) cc_final: 0.8344 (tt0) REVERT: T 325 MET cc_start: 0.8310 (tpp) cc_final: 0.7938 (tpp) REVERT: T 409 ASN cc_start: 0.8806 (t0) cc_final: 0.8441 (t0) REVERT: K 44 ASN cc_start: 0.7970 (m-40) cc_final: 0.7655 (m-40) REVERT: K 291 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: K 356 HIS cc_start: 0.8391 (m-70) cc_final: 0.8188 (m90) REVERT: A 250 ASP cc_start: 0.8396 (m-30) cc_final: 0.8031 (m-30) REVERT: A 375 MET cc_start: 0.8920 (tpp) cc_final: 0.8676 (mmm) REVERT: A 460 GLU cc_start: 0.6749 (mm-30) cc_final: 0.5946 (mm-30) REVERT: A 534 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8421 (pp) outliers start: 47 outliers final: 35 residues processed: 273 average time/residue: 0.1187 time to fit residues: 52.7034 Evaluate side-chains 271 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 209 GLN Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain U residue 381 SER Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.0020 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 230 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN K 45 ASN K 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086590 restraints weight = 28777.685| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.08 r_work: 0.2838 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19714 Z= 0.122 Angle : 0.577 10.724 26887 Z= 0.288 Chirality : 0.042 0.183 3088 Planarity : 0.005 0.103 3360 Dihedral : 5.807 73.528 2641 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.32 % Allowed : 12.35 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2384 helix: 1.28 (0.16), residues: 1059 sheet: -0.93 (0.25), residues: 385 loop : -1.49 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 71 TYR 0.020 0.001 TYR K 59 PHE 0.017 0.001 PHE T 381 TRP 0.015 0.001 TRP U 376 HIS 0.005 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (19703) covalent geometry : angle 0.57568 / 0.29 (26862) SS BOND : bond 0.00255 / 0.15 ( 5) SS BOND : angle 0.93348 / 0.49 ( 10) hydrogen bonds : bond 0.03553 / 2.31 ( 932) hydrogen bonds : angle 4.41989 / 3.12 ( 2871) Misc. bond : bond 0.00149 / 0.08 ( 1) link_BETA1-4 : bond 0.00434 / 0.21 ( 2) link_BETA1-4 : angle 1.53107 / 0.68 ( 6) link_NAG-ASN : bond 0.00293 / 0.14 ( 3) link_NAG-ASN : angle 1.99594 / 1.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 1 MET cc_start: 0.3337 (ttp) cc_final: 0.3100 (ttm) REVERT: S 72 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7525 (tm-30) REVERT: S 119 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6439 (tt) REVERT: S 179 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: S 206 ASP cc_start: 0.7680 (t0) cc_final: 0.7161 (t0) REVERT: S 269 SER cc_start: 0.8008 (t) cc_final: 0.7763 (t) REVERT: S 529 MET cc_start: 0.1309 (tmm) cc_final: 0.0025 (mtt) REVERT: T 277 GLU cc_start: 0.8674 (tt0) cc_final: 0.8374 (tt0) REVERT: T 325 MET cc_start: 0.8181 (tpp) cc_final: 0.7768 (tpp) REVERT: T 409 ASN cc_start: 0.8741 (t0) cc_final: 0.8221 (t0) REVERT: T 526 TYR cc_start: 0.8060 (t80) cc_final: 0.7639 (t80) REVERT: K 291 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: K 380 MET cc_start: 0.6835 (tmm) cc_final: 0.6599 (tmm) REVERT: A 123 MET cc_start: 0.8356 (mmm) cc_final: 0.8008 (mmm) REVERT: A 250 ASP cc_start: 0.8394 (m-30) cc_final: 0.8036 (m-30) REVERT: A 460 GLU cc_start: 0.6840 (mm-30) cc_final: 0.5963 (mm-30) REVERT: A 462 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: A 472 TYR cc_start: 0.8209 (t80) cc_final: 0.7955 (t80) REVERT: A 534 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8444 (pp) outliers start: 48 outliers final: 30 residues processed: 284 average time/residue: 0.1288 time to fit residues: 59.8356 Evaluate side-chains 275 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 209 GLN Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 527 ASN Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8724 > 50: distance: 15 - 29: 32.851 distance: 25 - 29: 34.414 distance: 29 - 30: 58.000 distance: 30 - 31: 61.427 distance: 30 - 33: 39.407 distance: 31 - 32: 26.953 distance: 31 - 37: 23.057 distance: 33 - 34: 48.239 distance: 33 - 35: 39.287 distance: 34 - 36: 46.109 distance: 37 - 38: 38.818 distance: 38 - 39: 39.790 distance: 38 - 41: 57.521 distance: 39 - 40: 41.085 distance: 39 - 45: 41.746 distance: 41 - 42: 57.091 distance: 42 - 43: 24.984 distance: 42 - 44: 41.100 distance: 45 - 46: 48.570 distance: 46 - 47: 36.963 distance: 46 - 49: 48.557 distance: 47 - 48: 55.830 distance: 47 - 51: 55.409 distance: 49 - 50: 47.848 distance: 51 - 52: 20.705 distance: 52 - 53: 23.889 distance: 52 - 55: 38.226 distance: 53 - 54: 12.944 distance: 53 - 58: 30.052 distance: 55 - 56: 12.086 distance: 55 - 57: 21.687 distance: 58 - 59: 10.948 distance: 59 - 60: 33.225 distance: 59 - 62: 17.100 distance: 60 - 61: 19.098 distance: 60 - 66: 17.617 distance: 62 - 63: 39.924 distance: 63 - 64: 23.015 distance: 63 - 65: 18.419 distance: 66 - 67: 30.124 distance: 68 - 69: 39.726 distance: 68 - 73: 57.118 distance: 70 - 71: 36.336 distance: 73 - 74: 11.130 distance: 74 - 75: 69.394 distance: 74 - 77: 55.594 distance: 75 - 76: 10.783 distance: 75 - 80: 57.800 distance: 77 - 78: 40.917 distance: 77 - 79: 39.790 distance: 80 - 81: 9.479 distance: 81 - 82: 41.390 distance: 81 - 84: 4.366 distance: 82 - 83: 41.007 distance: 82 - 87: 9.455 distance: 84 - 85: 56.690 distance: 84 - 86: 29.749 distance: 87 - 88: 3.738 distance: 87 - 93: 57.378 distance: 88 - 89: 53.614 distance: 88 - 91: 5.189 distance: 89 - 90: 21.419 distance: 89 - 94: 32.970 distance: 91 - 92: 32.405 distance: 92 - 93: 64.737 distance: 94 - 95: 20.300 distance: 95 - 96: 58.319 distance: 95 - 98: 45.952 distance: 96 - 97: 39.265 distance: 96 - 101: 33.642 distance: 98 - 99: 40.581 distance: 98 - 100: 39.492