Starting phenix.real_space_refine on Tue Nov 18 10:56:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6du8_8912/11_2025/6du8_8912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6du8_8912/11_2025/6du8_8912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6du8_8912/11_2025/6du8_8912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6du8_8912/11_2025/6du8_8912.map" model { file = "/net/cci-nas-00/data/ceres_data/6du8_8912/11_2025/6du8_8912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6du8_8912/11_2025/6du8_8912.cif" } resolution = 3.11 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 8880 2.51 5 N 2136 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3331 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 4 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 3, 'ASP:plan': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 2.83, per 1000 atoms: 0.21 Number of scatterers: 13380 At special positions: 0 Unit cell: (115.44, 115.44, 93.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2320 8.00 N 2136 7.00 C 8880 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM13336 O5 NAG A 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM13364 O5 NAG C 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM13378 O5 NAG D 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM13350 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 207 " " NAG B 901 " - " ASN B 207 " " NAG C 901 " - " ASN C 207 " " NAG D 901 " - " ASN D 207 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 571.0 milliseconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 48.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE A 151 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE A 359 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE B 151 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 396 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 452 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE B 486 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN B 516 " --> pdb=" O CYS B 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE C 151 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE C 359 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 368 " --> pdb=" O PHE C 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 406 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 452 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN C 516 " --> pdb=" O CYS C 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 520 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 521 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA C 558 " --> pdb=" O ASN C 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE D 151 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE D 359 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 361 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 363 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE D 364 " --> pdb=" O CYS D 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 396 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 406 " --> pdb=" O GLY D 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 452 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE D 486 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN D 516 " --> pdb=" O CYS D 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 521 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA D 558 " --> pdb=" O ASN D 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL A 300 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN A 309 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 314 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL B 300 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN B 309 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 314 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL C 300 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN C 309 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 314 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL D 300 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN D 309 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 314 " --> pdb=" O ASN D 309 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1608 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: 1.89 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3312 1.33 - 1.45: 3260 1.45 - 1.57: 7132 1.57 - 1.69: 4 1.69 - 1.81: 60 Bond restraints: 13768 Sorted by residual: bond pdb=" CA GLY B 500 " pdb=" C GLY B 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY A 500 " pdb=" C GLY A 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY D 500 " pdb=" C GLY D 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY C 500 " pdb=" C GLY C 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " ideal model delta sigma weight residual 1.532 1.570 -0.038 1.57e-02 4.06e+03 6.01e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 18128 2.73 - 5.47: 524 5.47 - 8.20: 96 8.20 - 10.93: 8 10.93 - 13.67: 8 Bond angle restraints: 18764 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS A 340 " pdb=" CA LYS A 340 " pdb=" C LYS A 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS C 340 " pdb=" CA LYS C 340 " pdb=" C LYS C 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS D 340 " pdb=" CA LYS D 340 " pdb=" C LYS D 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N GLY C 500 " pdb=" CA GLY C 500 " pdb=" C GLY C 500 " ideal model delta sigma weight residual 110.21 102.15 8.06 9.10e-01 1.21e+00 7.84e+01 ... (remaining 18759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 7084 15.72 - 31.43: 532 31.43 - 47.14: 120 47.14 - 62.86: 8 62.86 - 78.57: 12 Dihedral angle restraints: 7756 sinusoidal: 2848 harmonic: 4908 Sorted by residual: dihedral pdb=" CA TYR C 189 " pdb=" C TYR C 189 " pdb=" N TYR C 190 " pdb=" CA TYR C 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR A 189 " pdb=" C TYR A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR B 189 " pdb=" C TYR B 189 " pdb=" N TYR B 190 " pdb=" CA TYR B 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2080 0.185 - 0.370: 20 0.370 - 0.555: 0 0.555 - 0.740: 0 0.740 - 0.924: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" C1 NAG D 901 " pdb=" ND2 ASN D 207 " pdb=" C2 NAG D 901 " pdb=" O5 NAG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 207 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 207 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 ... (remaining 2101 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 207 " 0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN C 207 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN C 207 " 0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN C 207 " -0.536 2.00e-02 2.50e+03 pdb=" C1 NAG C 901 " 0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 207 " -0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN D 207 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN D 207 " -0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN D 207 " 0.536 2.00e-02 2.50e+03 pdb=" C1 NAG D 901 " -0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 207 " 0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN A 207 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN A 207 " 0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN A 207 " -0.536 2.00e-02 2.50e+03 pdb=" C1 NAG A 901 " 0.364 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 128 2.62 - 3.19: 11312 3.19 - 3.76: 20708 3.76 - 4.33: 26952 4.33 - 4.90: 44754 Nonbonded interactions: 103854 Sorted by model distance: nonbonded pdb=" CB PHE A 315 " pdb=" CD2 LEU A 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE C 315 " pdb=" CD2 LEU C 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE D 315 " pdb=" CD2 LEU D 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE B 315 " pdb=" CD2 LEU B 341 " model vdw 2.046 3.860 nonbonded pdb=" OD1 ASN C 505 " pdb=" OG1 THR C 515 " model vdw 2.218 3.040 ... (remaining 103849 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 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 0.069 13772 Z= 0.327 Angle : 1.450 49.708 18776 Z= 0.708 Chirality : 0.077 0.924 2104 Planarity : 0.007 0.067 2344 Dihedral : 12.525 78.570 4604 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.89 % Allowed : 5.62 % Favored : 93.49 % 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: -4.81 (0.16), residues: 1644 helix: -3.25 (0.12), residues: 764 sheet: -1.67 (0.40), residues: 168 loop : -3.42 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 206 TYR 0.054 0.005 TYR C 129 PHE 0.032 0.003 PHE D 305 TRP 0.032 0.003 TRP C 259 HIS 0.007 0.003 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00726 (13768) covalent geometry : angle 1.14155 (18764) hydrogen bonds : bond 0.14099 ( 544) hydrogen bonds : angle 7.56606 ( 1608) link_NAG-ASN : bond 0.00042 ( 4) link_NAG-ASN : angle 35.38520 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 400 time to evaluate : 0.445 Fit side-chains REVERT: A 186 SER cc_start: 0.8150 (m) cc_final: 0.7553 (p) REVERT: A 404 HIS cc_start: 0.7418 (m90) cc_final: 0.7214 (m90) REVERT: A 406 PHE cc_start: 0.8409 (t80) cc_final: 0.8070 (t80) REVERT: A 415 MET cc_start: 0.8326 (mpp) cc_final: 0.8106 (mmp) REVERT: A 435 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6752 (tt0) REVERT: A 527 ASN cc_start: 0.6423 (t0) cc_final: 0.6117 (t0) REVERT: B 186 SER cc_start: 0.8151 (m) cc_final: 0.7554 (p) REVERT: B 404 HIS cc_start: 0.7416 (m90) cc_final: 0.7214 (m90) REVERT: B 406 PHE cc_start: 0.8409 (t80) cc_final: 0.8070 (t80) REVERT: B 415 MET cc_start: 0.8328 (mpp) cc_final: 0.8104 (mmp) REVERT: B 435 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6754 (tt0) REVERT: B 527 ASN cc_start: 0.6420 (t0) cc_final: 0.6114 (t0) REVERT: C 186 SER cc_start: 0.8152 (m) cc_final: 0.7553 (p) REVERT: C 404 HIS cc_start: 0.7417 (m90) cc_final: 0.7216 (m90) REVERT: C 406 PHE cc_start: 0.8407 (t80) cc_final: 0.8069 (t80) REVERT: C 415 MET cc_start: 0.8323 (mpp) cc_final: 0.8104 (mmp) REVERT: C 435 GLN cc_start: 0.7232 (tp-100) cc_final: 0.6752 (tt0) REVERT: C 527 ASN cc_start: 0.6420 (t0) cc_final: 0.6116 (t0) REVERT: D 186 SER cc_start: 0.8151 (m) cc_final: 0.7553 (p) REVERT: D 404 HIS cc_start: 0.7419 (m90) cc_final: 0.7217 (m90) REVERT: D 406 PHE cc_start: 0.8409 (t80) cc_final: 0.8070 (t80) REVERT: D 415 MET cc_start: 0.8327 (mpp) cc_final: 0.8104 (mmp) REVERT: D 435 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6753 (tt0) REVERT: D 527 ASN cc_start: 0.6418 (t0) cc_final: 0.6113 (t0) outliers start: 12 outliers final: 12 residues processed: 412 average time/residue: 0.0944 time to fit residues: 60.8751 Evaluate side-chains 320 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 308 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 510 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 502 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 440 ASN B 502 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 502 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN D 502 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.174257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138935 restraints weight = 16231.397| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.65 r_work: 0.3888 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13772 Z= 0.149 Angle : 0.729 15.512 18776 Z= 0.372 Chirality : 0.054 0.605 2104 Planarity : 0.005 0.065 2344 Dihedral : 6.781 50.310 1924 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.55 % Allowed : 11.24 % Favored : 85.21 % 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: -3.44 (0.18), residues: 1644 helix: -1.83 (0.16), residues: 756 sheet: -1.00 (0.40), residues: 176 loop : -3.11 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 296 TYR 0.019 0.002 TYR B 129 PHE 0.016 0.002 PHE D 506 TRP 0.017 0.001 TRP A 434 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00337 (13768) covalent geometry : angle 0.68435 (18764) hydrogen bonds : bond 0.03829 ( 544) hydrogen bonds : angle 5.65056 ( 1608) link_NAG-ASN : bond 0.01001 ( 4) link_NAG-ASN : angle 9.98995 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 0.459 Fit side-chains REVERT: A 133 MET cc_start: 0.6605 (mmp) cc_final: 0.6190 (mmp) REVERT: A 186 SER cc_start: 0.8214 (m) cc_final: 0.7722 (p) REVERT: A 286 ARG cc_start: 0.6875 (tpt-90) cc_final: 0.6537 (ttp-170) REVERT: A 305 PHE cc_start: 0.6923 (p90) cc_final: 0.6351 (p90) REVERT: A 404 HIS cc_start: 0.7601 (m90) cc_final: 0.7180 (m90) REVERT: A 412 ASN cc_start: 0.7956 (m-40) cc_final: 0.7618 (t0) REVERT: A 431 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4162 (tp) REVERT: A 527 ASN cc_start: 0.6808 (t0) cc_final: 0.6484 (t0) REVERT: B 133 MET cc_start: 0.6604 (mmp) cc_final: 0.6188 (mmp) REVERT: B 186 SER cc_start: 0.8221 (m) cc_final: 0.7725 (p) REVERT: B 286 ARG cc_start: 0.6870 (tpt-90) cc_final: 0.6532 (ttp-170) REVERT: B 305 PHE cc_start: 0.6922 (p90) cc_final: 0.6346 (p90) REVERT: B 404 HIS cc_start: 0.7602 (m90) cc_final: 0.7182 (m90) REVERT: B 412 ASN cc_start: 0.7958 (m-40) cc_final: 0.7618 (t0) REVERT: B 431 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.4164 (tp) REVERT: B 527 ASN cc_start: 0.6804 (t0) cc_final: 0.6480 (t0) REVERT: C 133 MET cc_start: 0.6634 (mmp) cc_final: 0.6214 (mmp) REVERT: C 186 SER cc_start: 0.8217 (m) cc_final: 0.7729 (p) REVERT: C 286 ARG cc_start: 0.6882 (tpt-90) cc_final: 0.6543 (ttp-170) REVERT: C 305 PHE cc_start: 0.6934 (p90) cc_final: 0.6355 (p90) REVERT: C 404 HIS cc_start: 0.7598 (m90) cc_final: 0.7181 (m90) REVERT: C 412 ASN cc_start: 0.7956 (m-40) cc_final: 0.7614 (t0) REVERT: C 431 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.4163 (tp) REVERT: C 527 ASN cc_start: 0.6802 (t0) cc_final: 0.6478 (t0) REVERT: D 133 MET cc_start: 0.6615 (mmp) cc_final: 0.6200 (mmp) REVERT: D 186 SER cc_start: 0.8214 (m) cc_final: 0.7726 (p) REVERT: D 286 ARG cc_start: 0.6879 (tpt-90) cc_final: 0.6541 (ttp-170) REVERT: D 305 PHE cc_start: 0.6932 (p90) cc_final: 0.6359 (p90) REVERT: D 404 HIS cc_start: 0.7605 (m90) cc_final: 0.7189 (m90) REVERT: D 412 ASN cc_start: 0.7956 (m-40) cc_final: 0.7613 (t0) REVERT: D 431 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4167 (tp) REVERT: D 527 ASN cc_start: 0.6800 (t0) cc_final: 0.6476 (t0) outliers start: 48 outliers final: 20 residues processed: 364 average time/residue: 0.1017 time to fit residues: 57.0140 Evaluate side-chains 300 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 134 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 4.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN C 139 HIS ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.162959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127877 restraints weight = 16946.342| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.56 r_work: 0.3754 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13772 Z= 0.227 Angle : 0.812 14.703 18776 Z= 0.408 Chirality : 0.056 0.596 2104 Planarity : 0.005 0.061 2344 Dihedral : 6.128 28.982 1904 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 4.44 % Allowed : 14.28 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.84 (0.20), residues: 1644 helix: -1.09 (0.18), residues: 732 sheet: -0.95 (0.40), residues: 176 loop : -2.98 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.028 0.003 TYR C 129 PHE 0.023 0.002 PHE A 324 TRP 0.019 0.002 TRP A 259 HIS 0.005 0.002 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00536 (13768) covalent geometry : angle 0.77555 (18764) hydrogen bonds : bond 0.03859 ( 544) hydrogen bonds : angle 5.57134 ( 1608) link_NAG-ASN : bond 0.00862 ( 4) link_NAG-ASN : angle 9.58156 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 0.509 Fit side-chains REVERT: A 133 MET cc_start: 0.6481 (mmp) cc_final: 0.6113 (mmp) REVERT: A 186 SER cc_start: 0.8284 (m) cc_final: 0.7791 (p) REVERT: A 270 TYR cc_start: 0.7671 (m-80) cc_final: 0.7180 (m-80) REVERT: A 286 ARG cc_start: 0.7012 (tpt-90) cc_final: 0.6621 (ttp-170) REVERT: A 305 PHE cc_start: 0.6836 (p90) cc_final: 0.6514 (p90) REVERT: A 308 TYR cc_start: 0.6009 (t80) cc_final: 0.5703 (t80) REVERT: A 404 HIS cc_start: 0.7632 (m90) cc_final: 0.7151 (m90) REVERT: A 412 ASN cc_start: 0.8161 (m-40) cc_final: 0.7684 (t0) REVERT: A 485 PHE cc_start: 0.7816 (m-80) cc_final: 0.7098 (m-80) REVERT: A 527 ASN cc_start: 0.6993 (t0) cc_final: 0.6671 (t0) REVERT: B 133 MET cc_start: 0.6485 (mmp) cc_final: 0.6120 (mmp) REVERT: B 186 SER cc_start: 0.8271 (m) cc_final: 0.7775 (p) REVERT: B 270 TYR cc_start: 0.7669 (m-80) cc_final: 0.7182 (m-80) REVERT: B 286 ARG cc_start: 0.7021 (tpt-90) cc_final: 0.6629 (ttp-170) REVERT: B 305 PHE cc_start: 0.6842 (p90) cc_final: 0.6521 (p90) REVERT: B 308 TYR cc_start: 0.6015 (t80) cc_final: 0.5709 (t80) REVERT: B 404 HIS cc_start: 0.7629 (m90) cc_final: 0.7149 (m90) REVERT: B 412 ASN cc_start: 0.8158 (m-40) cc_final: 0.7681 (t0) REVERT: B 485 PHE cc_start: 0.7818 (m-80) cc_final: 0.7089 (m-80) REVERT: B 527 ASN cc_start: 0.6986 (t0) cc_final: 0.6665 (t0) REVERT: C 133 MET cc_start: 0.6505 (mmp) cc_final: 0.6132 (mmp) REVERT: C 186 SER cc_start: 0.8283 (m) cc_final: 0.7792 (p) REVERT: C 270 TYR cc_start: 0.7671 (m-80) cc_final: 0.7176 (m-80) REVERT: C 286 ARG cc_start: 0.7019 (tpt-90) cc_final: 0.6627 (ttp-170) REVERT: C 305 PHE cc_start: 0.6831 (p90) cc_final: 0.6512 (p90) REVERT: C 308 TYR cc_start: 0.6002 (t80) cc_final: 0.5696 (t80) REVERT: C 404 HIS cc_start: 0.7638 (m90) cc_final: 0.7158 (m90) REVERT: C 412 ASN cc_start: 0.8159 (m-40) cc_final: 0.7679 (t0) REVERT: C 485 PHE cc_start: 0.7815 (m-80) cc_final: 0.7100 (m-80) REVERT: C 527 ASN cc_start: 0.6983 (t0) cc_final: 0.6662 (t0) REVERT: D 133 MET cc_start: 0.6554 (mmp) cc_final: 0.6171 (mmp) REVERT: D 186 SER cc_start: 0.8278 (m) cc_final: 0.7780 (p) REVERT: D 270 TYR cc_start: 0.7672 (m-80) cc_final: 0.7181 (m-80) REVERT: D 286 ARG cc_start: 0.7027 (tpt-90) cc_final: 0.6633 (ttp-170) REVERT: D 305 PHE cc_start: 0.6831 (p90) cc_final: 0.6511 (p90) REVERT: D 308 TYR cc_start: 0.6008 (t80) cc_final: 0.5704 (t80) REVERT: D 404 HIS cc_start: 0.7640 (m90) cc_final: 0.7159 (m90) REVERT: D 412 ASN cc_start: 0.8156 (m-40) cc_final: 0.7675 (t0) REVERT: D 485 PHE cc_start: 0.7819 (m-80) cc_final: 0.7093 (m-80) REVERT: D 527 ASN cc_start: 0.6987 (t0) cc_final: 0.6668 (t0) outliers start: 60 outliers final: 32 residues processed: 352 average time/residue: 0.0933 time to fit residues: 51.7614 Evaluate side-chains 324 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.176628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.141007 restraints weight = 15929.085| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.59 r_work: 0.3905 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13772 Z= 0.134 Angle : 0.740 13.839 18776 Z= 0.357 Chirality : 0.051 0.532 2104 Planarity : 0.004 0.055 2344 Dihedral : 5.585 30.116 1904 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.40 % Allowed : 17.97 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.40 (0.20), residues: 1644 helix: -0.70 (0.19), residues: 724 sheet: -0.75 (0.39), residues: 176 loop : -2.76 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 296 TYR 0.022 0.002 TYR D 526 PHE 0.019 0.002 PHE D 305 TRP 0.014 0.001 TRP D 434 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00306 (13768) covalent geometry : angle 0.70399 (18764) hydrogen bonds : bond 0.03321 ( 544) hydrogen bonds : angle 5.33425 ( 1608) link_NAG-ASN : bond 0.01156 ( 4) link_NAG-ASN : angle 9.00756 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 0.683 Fit side-chains REVERT: A 186 SER cc_start: 0.8233 (m) cc_final: 0.7743 (p) REVERT: A 270 TYR cc_start: 0.7451 (m-80) cc_final: 0.7085 (m-80) REVERT: A 286 ARG cc_start: 0.6792 (tpt-90) cc_final: 0.6332 (ttm110) REVERT: A 305 PHE cc_start: 0.6809 (p90) cc_final: 0.6423 (p90) REVERT: A 404 HIS cc_start: 0.7410 (m90) cc_final: 0.6912 (m90) REVERT: A 412 ASN cc_start: 0.8142 (m-40) cc_final: 0.7645 (t0) REVERT: A 485 PHE cc_start: 0.7791 (m-80) cc_final: 0.7039 (m-80) REVERT: A 527 ASN cc_start: 0.7028 (t0) cc_final: 0.6700 (t0) REVERT: B 186 SER cc_start: 0.8233 (m) cc_final: 0.7740 (p) REVERT: B 270 TYR cc_start: 0.7452 (m-80) cc_final: 0.7086 (m-80) REVERT: B 286 ARG cc_start: 0.6803 (tpt-90) cc_final: 0.6337 (ttm110) REVERT: B 305 PHE cc_start: 0.6825 (p90) cc_final: 0.6421 (p90) REVERT: B 404 HIS cc_start: 0.7404 (m90) cc_final: 0.6906 (m90) REVERT: B 412 ASN cc_start: 0.8135 (m-40) cc_final: 0.7640 (t0) REVERT: B 485 PHE cc_start: 0.7787 (m-80) cc_final: 0.7034 (m-80) REVERT: B 527 ASN cc_start: 0.7016 (t0) cc_final: 0.6684 (t0) REVERT: C 186 SER cc_start: 0.8228 (m) cc_final: 0.7741 (p) REVERT: C 270 TYR cc_start: 0.7448 (m-80) cc_final: 0.7078 (m-80) REVERT: C 286 ARG cc_start: 0.6808 (tpt-90) cc_final: 0.6343 (ttm110) REVERT: C 305 PHE cc_start: 0.6831 (p90) cc_final: 0.6427 (p90) REVERT: C 404 HIS cc_start: 0.7405 (m90) cc_final: 0.6908 (m90) REVERT: C 412 ASN cc_start: 0.8141 (m-40) cc_final: 0.7646 (t0) REVERT: C 485 PHE cc_start: 0.7787 (m-80) cc_final: 0.7046 (m-80) REVERT: C 527 ASN cc_start: 0.7012 (t0) cc_final: 0.6681 (t0) REVERT: D 186 SER cc_start: 0.8233 (m) cc_final: 0.7745 (p) REVERT: D 270 TYR cc_start: 0.7454 (m-80) cc_final: 0.7088 (m-80) REVERT: D 286 ARG cc_start: 0.6815 (tpt-90) cc_final: 0.6346 (ttm110) REVERT: D 305 PHE cc_start: 0.6824 (p90) cc_final: 0.6424 (p90) REVERT: D 404 HIS cc_start: 0.7399 (m90) cc_final: 0.6901 (m90) REVERT: D 412 ASN cc_start: 0.8139 (m-40) cc_final: 0.7642 (t0) REVERT: D 485 PHE cc_start: 0.7783 (m-80) cc_final: 0.7039 (m-80) REVERT: D 527 ASN cc_start: 0.7016 (t0) cc_final: 0.6683 (t0) outliers start: 46 outliers final: 34 residues processed: 339 average time/residue: 0.0951 time to fit residues: 50.8394 Evaluate side-chains 324 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 120 optimal weight: 0.0010 chunk 3 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.180336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.144300 restraints weight = 16187.422| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.67 r_work: 0.3943 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13772 Z= 0.154 Angle : 0.729 14.312 18776 Z= 0.357 Chirality : 0.051 0.518 2104 Planarity : 0.004 0.057 2344 Dihedral : 5.532 27.732 1904 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.48 % Allowed : 22.41 % Favored : 74.11 % 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: -2.45 (0.20), residues: 1644 helix: -0.73 (0.19), residues: 752 sheet: -0.75 (0.39), residues: 176 loop : -2.87 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.021 0.002 TYR A 526 PHE 0.020 0.002 PHE D 305 TRP 0.012 0.001 TRP A 434 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00359 (13768) covalent geometry : angle 0.69591 (18764) hydrogen bonds : bond 0.03338 ( 544) hydrogen bonds : angle 5.22380 ( 1608) link_NAG-ASN : bond 0.01053 ( 4) link_NAG-ASN : angle 8.59190 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 0.526 Fit side-chains REVERT: A 186 SER cc_start: 0.8229 (m) cc_final: 0.7745 (p) REVERT: A 270 TYR cc_start: 0.7550 (m-80) cc_final: 0.7117 (m-80) REVERT: A 286 ARG cc_start: 0.6757 (tpt-90) cc_final: 0.6392 (ttp-170) REVERT: A 305 PHE cc_start: 0.6816 (p90) cc_final: 0.6442 (p90) REVERT: A 404 HIS cc_start: 0.7481 (m90) cc_final: 0.6911 (m90) REVERT: A 485 PHE cc_start: 0.7775 (m-80) cc_final: 0.7005 (m-80) REVERT: A 527 ASN cc_start: 0.7050 (t0) cc_final: 0.6761 (t0) REVERT: B 186 SER cc_start: 0.8232 (m) cc_final: 0.7744 (p) REVERT: B 270 TYR cc_start: 0.7546 (m-80) cc_final: 0.7116 (m-80) REVERT: B 286 ARG cc_start: 0.6763 (tpt-90) cc_final: 0.6394 (ttp-170) REVERT: B 305 PHE cc_start: 0.6822 (p90) cc_final: 0.6443 (p90) REVERT: B 404 HIS cc_start: 0.7480 (m90) cc_final: 0.6909 (m90) REVERT: B 485 PHE cc_start: 0.7775 (m-80) cc_final: 0.7001 (m-80) REVERT: C 186 SER cc_start: 0.8229 (m) cc_final: 0.7740 (p) REVERT: C 270 TYR cc_start: 0.7543 (m-80) cc_final: 0.7109 (m-80) REVERT: C 286 ARG cc_start: 0.6759 (tpt-90) cc_final: 0.6394 (ttp-170) REVERT: C 305 PHE cc_start: 0.6810 (p90) cc_final: 0.6431 (p90) REVERT: C 404 HIS cc_start: 0.7478 (m90) cc_final: 0.6909 (m90) REVERT: C 485 PHE cc_start: 0.7776 (m-80) cc_final: 0.7005 (m-80) REVERT: C 527 ASN cc_start: 0.7040 (t0) cc_final: 0.6750 (t0) REVERT: D 186 SER cc_start: 0.8230 (m) cc_final: 0.7744 (p) REVERT: D 270 TYR cc_start: 0.7551 (m-80) cc_final: 0.7118 (m-80) REVERT: D 286 ARG cc_start: 0.6773 (tpt-90) cc_final: 0.6401 (ttp-170) REVERT: D 305 PHE cc_start: 0.6811 (p90) cc_final: 0.6439 (p90) REVERT: D 404 HIS cc_start: 0.7476 (m90) cc_final: 0.6907 (m90) REVERT: D 485 PHE cc_start: 0.7774 (m-80) cc_final: 0.7001 (m-80) REVERT: D 527 ASN cc_start: 0.7036 (t0) cc_final: 0.6746 (t0) outliers start: 47 outliers final: 36 residues processed: 317 average time/residue: 0.0980 time to fit residues: 47.6229 Evaluate side-chains 309 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 60 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 192 ASN B 412 ASN C 412 ASN D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.174098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139202 restraints weight = 15885.161| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 3.54 r_work: 0.4002 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13772 Z= 0.113 Angle : 0.706 15.308 18776 Z= 0.337 Chirality : 0.048 0.481 2104 Planarity : 0.004 0.050 2344 Dihedral : 5.084 27.325 1904 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.99 % Allowed : 21.23 % Favored : 74.78 % 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: -2.19 (0.20), residues: 1644 helix: -0.56 (0.19), residues: 752 sheet: -0.44 (0.39), residues: 176 loop : -2.72 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.016 0.002 TYR D 526 PHE 0.031 0.001 PHE B 430 TRP 0.012 0.001 TRP D 434 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00237 (13768) covalent geometry : angle 0.67590 (18764) hydrogen bonds : bond 0.03243 ( 544) hydrogen bonds : angle 5.03873 ( 1608) link_NAG-ASN : bond 0.01308 ( 4) link_NAG-ASN : angle 8.16145 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 0.496 Fit side-chains REVERT: A 186 SER cc_start: 0.8232 (m) cc_final: 0.7755 (p) REVERT: A 216 PHE cc_start: 0.7061 (m-80) cc_final: 0.6668 (m-80) REVERT: A 270 TYR cc_start: 0.7232 (m-80) cc_final: 0.6872 (m-80) REVERT: A 286 ARG cc_start: 0.6684 (tpt-90) cc_final: 0.6318 (ttp-170) REVERT: A 404 HIS cc_start: 0.7302 (m90) cc_final: 0.6659 (m90) REVERT: A 409 LEU cc_start: 0.8245 (mp) cc_final: 0.7766 (tt) REVERT: A 412 ASN cc_start: 0.8076 (m110) cc_final: 0.7392 (t0) REVERT: A 446 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7413 (tt) REVERT: B 186 SER cc_start: 0.8219 (m) cc_final: 0.7739 (p) REVERT: B 216 PHE cc_start: 0.7054 (m-80) cc_final: 0.6650 (m-80) REVERT: B 270 TYR cc_start: 0.7230 (m-80) cc_final: 0.6874 (m-80) REVERT: B 286 ARG cc_start: 0.6693 (tpt-90) cc_final: 0.6322 (ttp-170) REVERT: B 404 HIS cc_start: 0.7302 (m90) cc_final: 0.6661 (m90) REVERT: B 409 LEU cc_start: 0.8244 (mp) cc_final: 0.7761 (tt) REVERT: B 412 ASN cc_start: 0.8075 (m110) cc_final: 0.7397 (t0) REVERT: B 446 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7412 (tt) REVERT: B 527 ASN cc_start: 0.7033 (t0) cc_final: 0.6718 (t0) REVERT: C 186 SER cc_start: 0.8227 (m) cc_final: 0.7749 (p) REVERT: C 270 TYR cc_start: 0.7228 (m-80) cc_final: 0.6871 (m-80) REVERT: C 286 ARG cc_start: 0.6683 (tpt-90) cc_final: 0.6315 (ttp-170) REVERT: C 404 HIS cc_start: 0.7301 (m90) cc_final: 0.6660 (m90) REVERT: C 409 LEU cc_start: 0.8245 (mp) cc_final: 0.7760 (tt) REVERT: C 412 ASN cc_start: 0.8074 (m110) cc_final: 0.7391 (t0) REVERT: C 446 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7410 (tt) REVERT: C 527 ASN cc_start: 0.7042 (t0) cc_final: 0.6725 (t0) REVERT: D 186 SER cc_start: 0.8236 (m) cc_final: 0.7753 (p) REVERT: D 270 TYR cc_start: 0.7242 (m-80) cc_final: 0.6881 (m-80) REVERT: D 286 ARG cc_start: 0.6682 (tpt-90) cc_final: 0.6315 (ttp-170) REVERT: D 404 HIS cc_start: 0.7297 (m90) cc_final: 0.6655 (m90) REVERT: D 409 LEU cc_start: 0.8245 (mp) cc_final: 0.7758 (tt) REVERT: D 412 ASN cc_start: 0.8074 (m110) cc_final: 0.7392 (t0) REVERT: D 446 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7410 (tt) REVERT: D 527 ASN cc_start: 0.7045 (t0) cc_final: 0.6730 (t0) outliers start: 54 outliers final: 36 residues processed: 325 average time/residue: 0.0963 time to fit residues: 48.8979 Evaluate side-chains 311 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN D 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.172003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.137065 restraints weight = 16208.666| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.57 r_work: 0.3894 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13772 Z= 0.169 Angle : 0.742 13.460 18776 Z= 0.364 Chirality : 0.051 0.479 2104 Planarity : 0.004 0.057 2344 Dihedral : 5.280 27.801 1904 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.29 % Allowed : 22.41 % Favored : 73.30 % 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: -2.14 (0.20), residues: 1644 helix: -0.50 (0.19), residues: 756 sheet: -0.66 (0.39), residues: 176 loop : -2.66 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.021 0.002 TYR D 526 PHE 0.031 0.002 PHE C 305 TRP 0.012 0.002 TRP C 434 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00394 (13768) covalent geometry : angle 0.71503 (18764) hydrogen bonds : bond 0.03309 ( 544) hydrogen bonds : angle 5.13868 ( 1608) link_NAG-ASN : bond 0.00993 ( 4) link_NAG-ASN : angle 7.90364 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.498 Fit side-chains REVERT: A 186 SER cc_start: 0.8146 (m) cc_final: 0.7704 (p) REVERT: A 270 TYR cc_start: 0.7566 (m-80) cc_final: 0.7056 (m-80) REVERT: A 286 ARG cc_start: 0.6730 (tpt-90) cc_final: 0.6364 (ttp-170) REVERT: A 296 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5771 (mpt-90) REVERT: A 305 PHE cc_start: 0.6895 (p90) cc_final: 0.6430 (p90) REVERT: A 404 HIS cc_start: 0.7557 (m90) cc_final: 0.6970 (m90) REVERT: A 446 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7416 (tt) REVERT: A 526 TYR cc_start: 0.6374 (t80) cc_final: 0.6039 (t80) REVERT: B 186 SER cc_start: 0.8220 (m) cc_final: 0.7760 (p) REVERT: B 270 TYR cc_start: 0.7562 (m-80) cc_final: 0.7062 (m-80) REVERT: B 286 ARG cc_start: 0.6731 (tpt-90) cc_final: 0.6363 (ttp-170) REVERT: B 296 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5781 (mpt-90) REVERT: B 305 PHE cc_start: 0.6886 (p90) cc_final: 0.6416 (p90) REVERT: B 404 HIS cc_start: 0.7559 (m90) cc_final: 0.6973 (m90) REVERT: B 446 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7410 (tt) REVERT: C 186 SER cc_start: 0.8149 (m) cc_final: 0.7702 (p) REVERT: C 216 PHE cc_start: 0.7189 (m-80) cc_final: 0.6875 (m-80) REVERT: C 270 TYR cc_start: 0.7564 (m-80) cc_final: 0.7038 (m-80) REVERT: C 286 ARG cc_start: 0.6724 (tpt-90) cc_final: 0.6359 (ttp-170) REVERT: C 296 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5776 (mpt-90) REVERT: C 305 PHE cc_start: 0.6882 (p90) cc_final: 0.6426 (p90) REVERT: C 404 HIS cc_start: 0.7559 (m90) cc_final: 0.6974 (m90) REVERT: C 446 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7419 (tt) REVERT: C 526 TYR cc_start: 0.6372 (t80) cc_final: 0.6036 (t80) REVERT: D 186 SER cc_start: 0.8150 (m) cc_final: 0.7703 (p) REVERT: D 216 PHE cc_start: 0.7171 (m-80) cc_final: 0.6883 (m-80) REVERT: D 270 TYR cc_start: 0.7585 (m-80) cc_final: 0.7073 (m-80) REVERT: D 286 ARG cc_start: 0.6720 (tpt-90) cc_final: 0.6352 (ttp-170) REVERT: D 296 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5792 (mpt-90) REVERT: D 305 PHE cc_start: 0.6911 (p90) cc_final: 0.6446 (p90) REVERT: D 404 HIS cc_start: 0.7563 (m90) cc_final: 0.6978 (m90) REVERT: D 446 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7416 (tt) outliers start: 58 outliers final: 42 residues processed: 309 average time/residue: 0.0972 time to fit residues: 46.4169 Evaluate side-chains 325 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.0020 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.171691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136923 restraints weight = 16008.030| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.52 r_work: 0.3926 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13772 Z= 0.146 Angle : 0.743 14.396 18776 Z= 0.360 Chirality : 0.050 0.468 2104 Planarity : 0.004 0.051 2344 Dihedral : 5.199 27.329 1904 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.81 % Allowed : 22.71 % Favored : 72.49 % 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: -2.04 (0.20), residues: 1644 helix: -0.45 (0.19), residues: 756 sheet: -0.54 (0.40), residues: 176 loop : -2.59 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 296 TYR 0.022 0.002 TYR B 526 PHE 0.032 0.002 PHE B 430 TRP 0.014 0.001 TRP A 434 HIS 0.003 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00332 (13768) covalent geometry : angle 0.71730 (18764) hydrogen bonds : bond 0.03305 ( 544) hydrogen bonds : angle 5.13340 ( 1608) link_NAG-ASN : bond 0.01064 ( 4) link_NAG-ASN : angle 7.72625 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 277 time to evaluate : 0.529 Fit side-chains REVERT: A 186 SER cc_start: 0.8025 (m) cc_final: 0.7597 (p) REVERT: A 216 PHE cc_start: 0.7240 (m-80) cc_final: 0.7015 (m-80) REVERT: A 270 TYR cc_start: 0.7588 (m-80) cc_final: 0.7065 (m-80) REVERT: A 283 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 286 ARG cc_start: 0.6843 (tpt-90) cc_final: 0.6377 (ttm110) REVERT: A 296 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5837 (mpt-90) REVERT: A 305 PHE cc_start: 0.6968 (p90) cc_final: 0.6457 (p90) REVERT: A 404 HIS cc_start: 0.7460 (m90) cc_final: 0.6778 (m90) REVERT: A 446 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7533 (tt) REVERT: B 186 SER cc_start: 0.8149 (m) cc_final: 0.7715 (p) REVERT: B 216 PHE cc_start: 0.7245 (m-80) cc_final: 0.7021 (m-80) REVERT: B 270 TYR cc_start: 0.7582 (m-80) cc_final: 0.7066 (m-80) REVERT: B 283 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 286 ARG cc_start: 0.6848 (tpt-90) cc_final: 0.6380 (ttm110) REVERT: B 296 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5838 (mpt-90) REVERT: B 305 PHE cc_start: 0.6924 (p90) cc_final: 0.6404 (p90) REVERT: B 404 HIS cc_start: 0.7461 (m90) cc_final: 0.6780 (m90) REVERT: B 446 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7532 (tt) REVERT: C 186 SER cc_start: 0.8023 (m) cc_final: 0.7595 (p) REVERT: C 216 PHE cc_start: 0.7175 (m-80) cc_final: 0.6885 (m-80) REVERT: C 270 TYR cc_start: 0.7603 (m-80) cc_final: 0.7086 (m-80) REVERT: C 283 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 286 ARG cc_start: 0.6839 (tpt-90) cc_final: 0.6376 (ttm110) REVERT: C 296 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5846 (mpt-90) REVERT: C 305 PHE cc_start: 0.6921 (p90) cc_final: 0.6419 (p90) REVERT: C 404 HIS cc_start: 0.7460 (m90) cc_final: 0.6777 (m90) REVERT: C 446 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7529 (tt) REVERT: C 503 VAL cc_start: 0.4115 (OUTLIER) cc_final: 0.3885 (p) REVERT: D 186 SER cc_start: 0.8032 (m) cc_final: 0.7594 (p) REVERT: D 216 PHE cc_start: 0.7172 (m-80) cc_final: 0.6910 (m-80) REVERT: D 270 TYR cc_start: 0.7598 (m-80) cc_final: 0.7079 (m-80) REVERT: D 283 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 286 ARG cc_start: 0.6843 (tpt-90) cc_final: 0.6376 (ttm110) REVERT: D 296 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5843 (mpt-90) REVERT: D 305 PHE cc_start: 0.6955 (p90) cc_final: 0.6436 (p90) REVERT: D 404 HIS cc_start: 0.7465 (m90) cc_final: 0.6785 (m90) REVERT: D 446 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7529 (tt) REVERT: D 503 VAL cc_start: 0.4057 (OUTLIER) cc_final: 0.3827 (p) outliers start: 65 outliers final: 44 residues processed: 318 average time/residue: 0.1060 time to fit residues: 51.0584 Evaluate side-chains 333 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 78 optimal weight: 0.0020 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 88 optimal weight: 0.0060 chunk 166 optimal weight: 0.7980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.175442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.140561 restraints weight = 16046.402| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.53 r_work: 0.4018 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13772 Z= 0.120 Angle : 0.722 14.628 18776 Z= 0.349 Chirality : 0.048 0.441 2104 Planarity : 0.004 0.050 2344 Dihedral : 4.758 25.314 1904 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.25 % Allowed : 24.04 % Favored : 72.71 % 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: -1.80 (0.20), residues: 1644 helix: -0.26 (0.19), residues: 768 sheet: -0.33 (0.40), residues: 176 loop : -2.51 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 296 TYR 0.017 0.002 TYR C 308 PHE 0.029 0.001 PHE C 305 TRP 0.012 0.001 TRP A 171 HIS 0.002 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00246 (13768) covalent geometry : angle 0.69785 (18764) hydrogen bonds : bond 0.03198 ( 544) hydrogen bonds : angle 5.04822 ( 1608) link_NAG-ASN : bond 0.01252 ( 4) link_NAG-ASN : angle 7.29642 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 311 time to evaluate : 0.489 Fit side-chains REVERT: A 216 PHE cc_start: 0.7256 (m-80) cc_final: 0.7032 (m-80) REVERT: A 283 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 286 ARG cc_start: 0.6665 (tpt-90) cc_final: 0.6245 (ttm110) REVERT: A 404 HIS cc_start: 0.7217 (m90) cc_final: 0.6532 (m90) REVERT: A 418 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7240 (mt) REVERT: A 435 GLN cc_start: 0.7510 (tp-100) cc_final: 0.7305 (tp40) REVERT: A 446 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7479 (tt) REVERT: B 186 SER cc_start: 0.8106 (m) cc_final: 0.7656 (p) REVERT: B 216 PHE cc_start: 0.7267 (m-80) cc_final: 0.7047 (m-80) REVERT: B 283 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 286 ARG cc_start: 0.6668 (tpt-90) cc_final: 0.6250 (ttm110) REVERT: B 305 PHE cc_start: 0.6738 (p90) cc_final: 0.6233 (p90) REVERT: B 404 HIS cc_start: 0.7208 (m90) cc_final: 0.6523 (m90) REVERT: B 418 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7312 (mt) REVERT: B 435 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7306 (tp40) REVERT: B 446 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7487 (tt) REVERT: B 527 ASN cc_start: 0.6956 (t0) cc_final: 0.6704 (t0) REVERT: C 216 PHE cc_start: 0.7343 (m-80) cc_final: 0.6941 (m-80) REVERT: C 283 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 286 ARG cc_start: 0.6669 (tpt-90) cc_final: 0.6251 (ttm110) REVERT: C 404 HIS cc_start: 0.7215 (m90) cc_final: 0.6530 (m90) REVERT: C 418 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7240 (mt) REVERT: C 446 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7453 (tt) REVERT: D 216 PHE cc_start: 0.7162 (m-80) cc_final: 0.6886 (m-80) REVERT: D 283 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7788 (mt-10) REVERT: D 286 ARG cc_start: 0.6671 (tpt-90) cc_final: 0.6252 (ttm110) REVERT: D 305 PHE cc_start: 0.6735 (p90) cc_final: 0.6233 (p90) REVERT: D 404 HIS cc_start: 0.7217 (m90) cc_final: 0.6533 (m90) REVERT: D 418 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7308 (mt) REVERT: D 435 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7307 (tp40) REVERT: D 446 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7487 (tt) outliers start: 44 outliers final: 30 residues processed: 335 average time/residue: 0.1030 time to fit residues: 53.2123 Evaluate side-chains 308 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.176421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.141451 restraints weight = 15813.593| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.62 r_work: 0.3881 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13772 Z= 0.183 Angle : 0.805 14.299 18776 Z= 0.394 Chirality : 0.052 0.444 2104 Planarity : 0.005 0.059 2344 Dihedral : 5.206 26.270 1904 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.40 % Allowed : 26.26 % Favored : 70.34 % 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: -1.86 (0.21), residues: 1644 helix: -0.27 (0.19), residues: 752 sheet: -0.44 (0.39), residues: 176 loop : -2.53 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.041 0.003 TYR D 128 PHE 0.036 0.002 PHE C 305 TRP 0.013 0.002 TRP D 434 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00424 (13768) covalent geometry : angle 0.78405 (18764) hydrogen bonds : bond 0.03509 ( 544) hydrogen bonds : angle 5.20360 ( 1608) link_NAG-ASN : bond 0.00949 ( 4) link_NAG-ASN : angle 7.27220 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 284 time to evaluate : 0.510 Fit side-chains REVERT: A 216 PHE cc_start: 0.7263 (m-80) cc_final: 0.7006 (m-80) REVERT: A 270 TYR cc_start: 0.7666 (m-80) cc_final: 0.7077 (m-80) REVERT: A 283 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 286 ARG cc_start: 0.6828 (tpt-90) cc_final: 0.6364 (ttm110) REVERT: A 366 TYR cc_start: 0.7143 (m-80) cc_final: 0.6750 (m-80) REVERT: A 404 HIS cc_start: 0.7605 (m90) cc_final: 0.6864 (m90) REVERT: A 435 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7406 (tp40) REVERT: A 446 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7484 (tt) REVERT: A 526 TYR cc_start: 0.6579 (t80) cc_final: 0.6284 (t80) REVERT: B 127 TYR cc_start: 0.6524 (p90) cc_final: 0.5903 (p90) REVERT: B 186 SER cc_start: 0.8066 (m) cc_final: 0.7661 (p) REVERT: B 216 PHE cc_start: 0.7275 (m-80) cc_final: 0.7023 (m-80) REVERT: B 270 TYR cc_start: 0.7674 (m-80) cc_final: 0.7092 (m-80) REVERT: B 283 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 286 ARG cc_start: 0.6817 (tpt-90) cc_final: 0.6342 (ttm110) REVERT: B 305 PHE cc_start: 0.6926 (p90) cc_final: 0.6527 (p90) REVERT: B 366 TYR cc_start: 0.7143 (m-80) cc_final: 0.6750 (m-80) REVERT: B 404 HIS cc_start: 0.7609 (m90) cc_final: 0.6869 (m90) REVERT: B 435 GLN cc_start: 0.7626 (tp-100) cc_final: 0.7309 (tp40) REVERT: B 446 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7481 (tt) REVERT: B 526 TYR cc_start: 0.6555 (t80) cc_final: 0.6301 (t80) REVERT: C 216 PHE cc_start: 0.7402 (m-80) cc_final: 0.6985 (m-80) REVERT: C 270 TYR cc_start: 0.7647 (m-80) cc_final: 0.7133 (m-80) REVERT: C 283 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 286 ARG cc_start: 0.6828 (tpt-90) cc_final: 0.6365 (ttm110) REVERT: C 366 TYR cc_start: 0.7140 (m-80) cc_final: 0.6746 (m-80) REVERT: C 404 HIS cc_start: 0.7612 (m90) cc_final: 0.6866 (m90) REVERT: C 446 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7480 (tt) REVERT: C 526 TYR cc_start: 0.6575 (t80) cc_final: 0.6281 (t80) REVERT: D 127 TYR cc_start: 0.6464 (p90) cc_final: 0.5863 (p90) REVERT: D 216 PHE cc_start: 0.7241 (m-80) cc_final: 0.6951 (m-80) REVERT: D 270 TYR cc_start: 0.7669 (m-80) cc_final: 0.7160 (m-80) REVERT: D 283 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7878 (mt-10) REVERT: D 286 ARG cc_start: 0.6825 (tpt-90) cc_final: 0.6361 (ttm110) REVERT: D 305 PHE cc_start: 0.6929 (p90) cc_final: 0.6508 (p90) REVERT: D 366 TYR cc_start: 0.7142 (m-80) cc_final: 0.6748 (m-80) REVERT: D 404 HIS cc_start: 0.7602 (m90) cc_final: 0.6860 (m90) REVERT: D 435 GLN cc_start: 0.7600 (tp-100) cc_final: 0.7390 (tp40) REVERT: D 446 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7484 (tt) REVERT: D 526 TYR cc_start: 0.6560 (t80) cc_final: 0.6309 (t80) outliers start: 46 outliers final: 36 residues processed: 308 average time/residue: 0.0977 time to fit residues: 47.6071 Evaluate side-chains 321 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.174204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139175 restraints weight = 15930.414| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.55 r_work: 0.4004 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13772 Z= 0.130 Angle : 0.746 15.475 18776 Z= 0.364 Chirality : 0.049 0.432 2104 Planarity : 0.004 0.047 2344 Dihedral : 4.894 24.439 1904 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.18 % Allowed : 25.74 % Favored : 71.08 % 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: -1.70 (0.21), residues: 1644 helix: -0.20 (0.19), residues: 768 sheet: -0.27 (0.40), residues: 176 loop : -2.45 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.028 0.002 TYR D 128 PHE 0.036 0.001 PHE C 305 TRP 0.012 0.001 TRP B 434 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00280 (13768) covalent geometry : angle 0.72440 (18764) hydrogen bonds : bond 0.03264 ( 544) hydrogen bonds : angle 5.11412 ( 1608) link_NAG-ASN : bond 0.01130 ( 4) link_NAG-ASN : angle 7.04043 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.50 seconds wall clock time: 75 minutes 18.47 seconds (4518.47 seconds total)