Starting phenix.real_space_refine on Sat Sep 12 03:48:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_8912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_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_8912/09_2026/6du8_8912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_8912.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_8912.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_8912.cif" model { file = "/net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_8912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6du8_8912/09_2026/6du8_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 3.59, per 1000 atoms: 0.27 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: 1.10 Conformation dependent library (CDL) restraints added in 667.4 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: 0.46 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: 2.02 Time building geometry restraints manager: 1.52 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: 7008 15.72 - 31.43: 524 31.43 - 47.14: 120 47.14 - 62.86: 8 62.86 - 78.57: 12 Dihedral angle restraints: 7672 sinusoidal: 2764 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 7669 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 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 : 12.565 78.570 4520 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/Z covalent geometry : bond 0.00726 / 0.33 (13768) covalent geometry : angle 1.14155 / 0.64 (18764) hydrogen bonds : bond 0.14099 / 9.33 ( 544) hydrogen bonds : angle 7.56606 / 5.25 ( 1608) link_NAG-ASN : bond 0.00042 / 0.02 ( 4) link_NAG-ASN : angle 35.38520 / 21.41 ( 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 : 0.434 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: 0.7215 (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: 0.8326 (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: 0.0940 time to fit residues: 61.0822 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 : 0.478 ------------------------------------------------------------------------------- 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... ** 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 435 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.173286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137974 restraints weight = 16292.690| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.60 r_work: 0.3867 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.1839 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 : 0.737 15.117 18776 Z= 0.376 Chirality : 0.055 0.641 2104 Planarity : 0.005 0.065 2344 Dihedral : 6.757 50.940 1840 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.25 % Allowed : 11.54 % 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: -3.54 (0.18), residues: 1644 helix: -1.93 (0.16), residues: 768 sheet: -1.04 (0.40), residues: 176 loop : -3.14 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 296 TYR 0.020 0.002 TYR A 129 PHE 0.017 0.002 PHE D 506 TRP 0.017 0.001 TRP C 434 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13768) covalent geometry : angle 0.69338 / 0.37 (18764) hydrogen bonds : bond 0.03865 / 2.55 ( 544) hydrogen bonds : angle 5.70852 / 3.95 ( 1608) link_NAG-ASN : bond 0.00607 / 0.30 ( 4) link_NAG-ASN : angle 9.96107 / 6.11 ( 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 372 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.384 Fit side-chains REVERT: A 133 MET cc_start: 0.6567 (mmp) cc_final: 0.6000 (mmp) REVERT: A 186 SER cc_start: 0.8191 (m) cc_final: 0.7714 (p) REVERT: A 305 PHE cc_start: 0.7063 (p90) cc_final: 0.6427 (p90) REVERT: A 404 HIS cc_start: 0.7605 (m90) cc_final: 0.7196 (m90) REVERT: A 406 PHE cc_start: 0.8311 (t80) cc_final: 0.8075 (t80) REVERT: A 412 ASN cc_start: 0.7956 (m-40) cc_final: 0.7609 (t0) REVERT: A 431 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.4107 (tp) REVERT: A 527 ASN cc_start: 0.6789 (t0) cc_final: 0.6455 (t0) REVERT: B 133 MET cc_start: 0.6578 (mmp) cc_final: 0.6003 (mmp) REVERT: B 186 SER cc_start: 0.8198 (m) cc_final: 0.7720 (p) REVERT: B 305 PHE cc_start: 0.7059 (p90) cc_final: 0.6427 (p90) REVERT: B 404 HIS cc_start: 0.7610 (m90) cc_final: 0.7200 (m90) REVERT: B 406 PHE cc_start: 0.8310 (t80) cc_final: 0.8077 (t80) REVERT: B 412 ASN cc_start: 0.7956 (m-40) cc_final: 0.7606 (t0) REVERT: B 431 LEU cc_start: 0.5282 (OUTLIER) cc_final: 0.4108 (tp) REVERT: B 527 ASN cc_start: 0.6789 (t0) cc_final: 0.6457 (t0) REVERT: C 133 MET cc_start: 0.6589 (mmp) cc_final: 0.6015 (mmp) REVERT: C 186 SER cc_start: 0.8196 (m) cc_final: 0.7726 (p) REVERT: C 305 PHE cc_start: 0.7073 (p90) cc_final: 0.6439 (p90) REVERT: C 404 HIS cc_start: 0.7604 (m90) cc_final: 0.7196 (m90) REVERT: C 406 PHE cc_start: 0.8315 (t80) cc_final: 0.8079 (t80) REVERT: C 412 ASN cc_start: 0.7956 (m-40) cc_final: 0.7607 (t0) REVERT: C 431 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4110 (tp) REVERT: C 527 ASN cc_start: 0.6793 (t0) cc_final: 0.6460 (t0) REVERT: D 133 MET cc_start: 0.6600 (mmp) cc_final: 0.6024 (mmp) REVERT: D 186 SER cc_start: 0.8189 (m) cc_final: 0.7720 (p) REVERT: D 305 PHE cc_start: 0.7071 (p90) cc_final: 0.6440 (p90) REVERT: D 404 HIS cc_start: 0.7607 (m90) cc_final: 0.7200 (m90) REVERT: D 406 PHE cc_start: 0.8315 (t80) cc_final: 0.8081 (t80) REVERT: D 412 ASN cc_start: 0.7955 (m-40) cc_final: 0.7605 (t0) REVERT: D 431 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.4115 (tp) REVERT: D 527 ASN cc_start: 0.6790 (t0) cc_final: 0.6457 (t0) outliers start: 44 outliers final: 12 residues processed: 356 average time/residue: 0.0931 time to fit residues: 52.5550 Evaluate side-chains 296 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU 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 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 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 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: 0.9980 chunk 102 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 55 optimal weight: 0.0170 chunk 154 optimal weight: 3.9990 chunk 134 optimal weight: 0.0870 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4344 r_free = 0.4344 target = 0.171705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135640 restraints weight = 16176.953| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.67 r_work: 0.3854 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.2397 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= 0.140 Angle : 0.731 14.730 18776 Z= 0.360 Chirality : 0.052 0.531 2104 Planarity : 0.005 0.058 2344 Dihedral : 5.428 28.213 1820 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.55 % Allowed : 14.79 % Favored : 81.66 % 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: -2.67 (0.19), residues: 1644 helix: -1.02 (0.18), residues: 728 sheet: -0.64 (0.40), residues: 176 loop : -2.87 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.016 0.002 TYR A 129 PHE 0.023 0.002 PHE D 433 TRP 0.015 0.001 TRP A 434 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13768) covalent geometry : angle 0.69155 / 0.35 (18764) hydrogen bonds : bond 0.03496 / 2.30 ( 544) hydrogen bonds : angle 5.34167 / 3.70 ( 1608) link_NAG-ASN : bond 0.01072 / 0.54 ( 4) link_NAG-ASN : angle 9.45002 / 5.81 ( 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: 48 poor density : 324 time to evaluate : 0.496 Fit side-chains REVERT: A 186 SER cc_start: 0.8246 (m) cc_final: 0.7720 (p) REVERT: A 286 ARG cc_start: 0.6925 (tpt-90) cc_final: 0.6527 (ttp-170) REVERT: A 404 HIS cc_start: 0.7564 (m90) cc_final: 0.7095 (m90) REVERT: A 412 ASN cc_start: 0.8094 (m-40) cc_final: 0.7686 (t0) REVERT: A 485 PHE cc_start: 0.7773 (m-80) cc_final: 0.7034 (m-80) REVERT: A 527 ASN cc_start: 0.6874 (t0) cc_final: 0.6558 (t0) REVERT: B 186 SER cc_start: 0.8242 (m) cc_final: 0.7713 (p) REVERT: B 286 ARG cc_start: 0.6932 (tpt-90) cc_final: 0.6532 (ttp-170) REVERT: B 404 HIS cc_start: 0.7555 (m90) cc_final: 0.7085 (m90) REVERT: B 412 ASN cc_start: 0.8100 (m-40) cc_final: 0.7689 (t0) REVERT: B 485 PHE cc_start: 0.7769 (m-80) cc_final: 0.7036 (m-80) REVERT: B 527 ASN cc_start: 0.6856 (t0) cc_final: 0.6541 (t0) REVERT: C 186 SER cc_start: 0.8246 (m) cc_final: 0.7715 (p) REVERT: C 286 ARG cc_start: 0.6934 (tpt-90) cc_final: 0.6532 (ttp-170) REVERT: C 404 HIS cc_start: 0.7570 (m90) cc_final: 0.7103 (m90) REVERT: C 412 ASN cc_start: 0.8095 (m-40) cc_final: 0.7684 (t0) REVERT: C 485 PHE cc_start: 0.7773 (m-80) cc_final: 0.7039 (m-80) REVERT: C 527 ASN cc_start: 0.6862 (t0) cc_final: 0.6546 (t0) REVERT: D 186 SER cc_start: 0.8245 (m) cc_final: 0.7717 (p) REVERT: D 286 ARG cc_start: 0.6938 (tpt-90) cc_final: 0.6536 (ttp-170) REVERT: D 404 HIS cc_start: 0.7558 (m90) cc_final: 0.7090 (m90) REVERT: D 412 ASN cc_start: 0.8098 (m-40) cc_final: 0.7686 (t0) REVERT: D 485 PHE cc_start: 0.7771 (m-80) cc_final: 0.7037 (m-80) REVERT: D 527 ASN cc_start: 0.6858 (t0) cc_final: 0.6544 (t0) outliers start: 48 outliers final: 28 residues processed: 344 average time/residue: 0.1018 time to fit residues: 54.1283 Evaluate side-chains 340 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 312 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 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 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 C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU 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 D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4345 r_free = 0.4345 target = 0.170979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.135480 restraints weight = 16148.512| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.64 r_work: 0.3910 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13772 Z= 0.145 Angle : 0.707 13.649 18776 Z= 0.352 Chirality : 0.051 0.506 2104 Planarity : 0.004 0.060 2344 Dihedral : 5.192 25.508 1820 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.14 % Allowed : 15.98 % Favored : 79.88 % 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: -2.40 (0.20), residues: 1644 helix: -0.76 (0.19), residues: 724 sheet: -0.63 (0.39), residues: 176 loop : -2.71 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.024 0.002 TYR C 526 PHE 0.032 0.002 PHE C 305 TRP 0.010 0.001 TRP C 434 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13768) covalent geometry : angle 0.67074 / 0.34 (18764) hydrogen bonds : bond 0.03367 / 2.22 ( 544) hydrogen bonds : angle 5.20078 / 3.60 ( 1608) link_NAG-ASN : bond 0.01026 / 0.51 ( 4) link_NAG-ASN : angle 8.85872 / 5.45 ( 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 374 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 0.482 Fit side-chains REVERT: A 186 SER cc_start: 0.8264 (m) cc_final: 0.7764 (p) REVERT: A 270 TYR cc_start: 0.7370 (m-80) cc_final: 0.7000 (m-80) REVERT: A 286 ARG cc_start: 0.6912 (tpt-90) cc_final: 0.6508 (ttp-170) REVERT: A 305 PHE cc_start: 0.6909 (p90) cc_final: 0.6479 (p90) REVERT: A 404 HIS cc_start: 0.7519 (m90) cc_final: 0.6968 (m90) REVERT: A 406 PHE cc_start: 0.8088 (t80) cc_final: 0.7819 (t80) REVERT: A 412 ASN cc_start: 0.8135 (m-40) cc_final: 0.7656 (t0) REVERT: B 133 MET cc_start: 0.6501 (mmp) cc_final: 0.6092 (mmp) REVERT: B 186 SER cc_start: 0.8267 (m) cc_final: 0.7765 (p) REVERT: B 270 TYR cc_start: 0.7376 (m-80) cc_final: 0.7006 (m-80) REVERT: B 286 ARG cc_start: 0.6915 (tpt-90) cc_final: 0.6512 (ttp-170) REVERT: B 305 PHE cc_start: 0.6906 (p90) cc_final: 0.6481 (p90) REVERT: B 404 HIS cc_start: 0.7521 (m90) cc_final: 0.6969 (m90) REVERT: B 406 PHE cc_start: 0.8090 (t80) cc_final: 0.7815 (t80) REVERT: B 412 ASN cc_start: 0.8133 (m-40) cc_final: 0.7653 (t0) REVERT: C 186 SER cc_start: 0.8260 (m) cc_final: 0.7760 (p) REVERT: C 270 TYR cc_start: 0.7372 (m-80) cc_final: 0.6994 (m-80) REVERT: C 286 ARG cc_start: 0.6910 (tpt-90) cc_final: 0.6508 (ttp-170) REVERT: C 305 PHE cc_start: 0.6917 (p90) cc_final: 0.6480 (p90) REVERT: C 404 HIS cc_start: 0.7525 (m90) cc_final: 0.6979 (m90) REVERT: C 406 PHE cc_start: 0.8093 (t80) cc_final: 0.7820 (t80) REVERT: C 412 ASN cc_start: 0.8138 (m-40) cc_final: 0.7657 (t0) REVERT: D 133 MET cc_start: 0.6520 (mmp) cc_final: 0.6104 (mmp) REVERT: D 186 SER cc_start: 0.8261 (m) cc_final: 0.7762 (p) REVERT: D 270 TYR cc_start: 0.7380 (m-80) cc_final: 0.7002 (m-80) REVERT: D 286 ARG cc_start: 0.6920 (tpt-90) cc_final: 0.6514 (ttp-170) REVERT: D 305 PHE cc_start: 0.6908 (p90) cc_final: 0.6475 (p90) REVERT: D 404 HIS cc_start: 0.7519 (m90) cc_final: 0.6972 (m90) REVERT: D 406 PHE cc_start: 0.8090 (t80) cc_final: 0.7815 (t80) REVERT: D 412 ASN cc_start: 0.8133 (m-40) cc_final: 0.7652 (t0) outliers start: 56 outliers final: 44 residues processed: 342 average time/residue: 0.0929 time to fit residues: 50.1637 Evaluate side-chains 336 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 397 SER Chi-restraints excluded: chain A residue 418 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 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 397 SER Chi-restraints excluded: chain B residue 418 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 262 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 397 SER Chi-restraints excluded: chain C residue 418 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 262 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 397 SER Chi-restraints excluded: chain D residue 418 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: 9.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN B 192 ASN D 192 ASN D 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.169162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.133156 restraints weight = 16498.012| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.58 r_work: 0.3851 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2936 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= 0.176 Angle : 0.736 12.898 18776 Z= 0.366 Chirality : 0.052 0.488 2104 Planarity : 0.005 0.057 2344 Dihedral : 5.249 23.735 1820 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.66 % Allowed : 17.68 % Favored : 77.66 % 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: -2.30 (0.20), residues: 1644 helix: -0.63 (0.19), residues: 732 sheet: -0.73 (0.39), residues: 176 loop : -2.69 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.023 0.003 TYR D 526 PHE 0.026 0.002 PHE A 305 TRP 0.016 0.002 TRP C 434 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (13768) covalent geometry : angle 0.70510 / 0.36 (18764) hydrogen bonds : bond 0.03432 / 2.26 ( 544) hydrogen bonds : angle 5.26157 / 3.64 ( 1608) link_NAG-ASN : bond 0.00892 / 0.45 ( 4) link_NAG-ASN : angle 8.41126 / 5.18 ( 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 347 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 0.500 Fit side-chains REVERT: A 133 MET cc_start: 0.6495 (mmp) cc_final: 0.6227 (mmt) REVERT: A 186 SER cc_start: 0.8235 (m) cc_final: 0.7769 (p) REVERT: A 216 PHE cc_start: 0.7501 (m-80) cc_final: 0.7086 (m-80) REVERT: A 270 TYR cc_start: 0.7624 (m-80) cc_final: 0.7125 (m-80) REVERT: A 283 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 286 ARG cc_start: 0.6888 (tpt-90) cc_final: 0.6315 (ttm110) REVERT: A 305 PHE cc_start: 0.6938 (p90) cc_final: 0.6514 (p90) REVERT: A 404 HIS cc_start: 0.7562 (m90) cc_final: 0.7046 (m90) REVERT: A 526 TYR cc_start: 0.6440 (t80) cc_final: 0.5998 (t80) REVERT: B 133 MET cc_start: 0.6445 (mmp) cc_final: 0.6178 (mmt) REVERT: B 186 SER cc_start: 0.8233 (m) cc_final: 0.7765 (p) REVERT: B 216 PHE cc_start: 0.7497 (m-80) cc_final: 0.7080 (m-80) REVERT: B 270 TYR cc_start: 0.7620 (m-80) cc_final: 0.7121 (m-80) REVERT: B 283 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7785 (mt-10) REVERT: B 286 ARG cc_start: 0.6892 (tpt-90) cc_final: 0.6314 (ttm110) REVERT: B 305 PHE cc_start: 0.6935 (p90) cc_final: 0.6517 (p90) REVERT: B 404 HIS cc_start: 0.7564 (m90) cc_final: 0.7047 (m90) REVERT: B 526 TYR cc_start: 0.6437 (t80) cc_final: 0.5995 (t80) REVERT: C 186 SER cc_start: 0.8229 (m) cc_final: 0.7763 (p) REVERT: C 270 TYR cc_start: 0.7618 (m-80) cc_final: 0.7121 (m-80) REVERT: C 283 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7788 (mt-10) REVERT: C 286 ARG cc_start: 0.6893 (tpt-90) cc_final: 0.6318 (ttm110) REVERT: C 305 PHE cc_start: 0.6935 (p90) cc_final: 0.6508 (p90) REVERT: C 404 HIS cc_start: 0.7567 (m90) cc_final: 0.7054 (m90) REVERT: C 526 TYR cc_start: 0.6426 (t80) cc_final: 0.6036 (t80) REVERT: D 133 MET cc_start: 0.6464 (mmp) cc_final: 0.6198 (mmt) REVERT: D 186 SER cc_start: 0.8231 (m) cc_final: 0.7763 (p) REVERT: D 270 TYR cc_start: 0.7621 (m-80) cc_final: 0.7125 (m-80) REVERT: D 283 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7792 (mt-10) REVERT: D 286 ARG cc_start: 0.6893 (tpt-90) cc_final: 0.6316 (ttm110) REVERT: D 305 PHE cc_start: 0.6932 (p90) cc_final: 0.6513 (p90) REVERT: D 404 HIS cc_start: 0.7565 (m90) cc_final: 0.7051 (m90) REVERT: D 526 TYR cc_start: 0.6414 (t80) cc_final: 0.5970 (t80) outliers start: 63 outliers final: 44 residues processed: 323 average time/residue: 0.0989 time to fit residues: 49.5009 Evaluate side-chains 331 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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 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 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 262 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 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 262 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 487 VAL Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 60 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN A 412 ASN B 192 ASN B 412 ASN C 412 ASN D 192 ASN D 412 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.175240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.139603 restraints weight = 15975.259| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 3.60 r_work: 0.3948 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13772 Z= 0.125 Angle : 0.704 14.923 18776 Z= 0.342 Chirality : 0.049 0.454 2104 Planarity : 0.004 0.053 2344 Dihedral : 4.848 21.958 1820 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.96 % Allowed : 19.53 % Favored : 75.52 % 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: -2.06 (0.20), residues: 1644 helix: -0.50 (0.19), residues: 740 sheet: -0.57 (0.39), residues: 176 loop : -2.50 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.017 0.002 TYR A 308 PHE 0.024 0.002 PHE C 305 TRP 0.012 0.001 TRP C 434 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13768) covalent geometry : angle 0.67540 / 0.34 (18764) hydrogen bonds : bond 0.03210 / 2.14 ( 544) hydrogen bonds : angle 5.13322 / 3.56 ( 1608) link_NAG-ASN : bond 0.01054 / 0.53 ( 4) link_NAG-ASN : angle 7.89963 / 4.85 ( 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 369 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 0.489 Fit side-chains REVERT: A 186 SER cc_start: 0.8207 (m) cc_final: 0.7755 (p) REVERT: A 216 PHE cc_start: 0.7397 (m-80) cc_final: 0.7021 (m-80) REVERT: A 270 TYR cc_start: 0.7410 (m-80) cc_final: 0.6992 (m-80) REVERT: A 283 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 286 ARG cc_start: 0.6894 (tpt-90) cc_final: 0.6313 (ttm110) REVERT: A 305 PHE cc_start: 0.6850 (p90) cc_final: 0.6352 (p90) REVERT: A 404 HIS cc_start: 0.7358 (m90) cc_final: 0.6806 (m90) REVERT: B 186 SER cc_start: 0.8204 (m) cc_final: 0.7752 (p) REVERT: B 216 PHE cc_start: 0.7397 (m-80) cc_final: 0.7020 (m-80) REVERT: B 270 TYR cc_start: 0.7410 (m-80) cc_final: 0.6995 (m-80) REVERT: B 283 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 286 ARG cc_start: 0.6898 (tpt-90) cc_final: 0.6311 (ttm110) REVERT: B 305 PHE cc_start: 0.6834 (p90) cc_final: 0.6420 (p90) REVERT: B 404 HIS cc_start: 0.7359 (m90) cc_final: 0.6806 (m90) REVERT: C 186 SER cc_start: 0.8211 (m) cc_final: 0.7765 (p) REVERT: C 216 PHE cc_start: 0.7469 (m-80) cc_final: 0.6593 (m-80) REVERT: C 270 TYR cc_start: 0.7411 (m-80) cc_final: 0.6994 (m-80) REVERT: C 283 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7714 (mt-10) REVERT: C 286 ARG cc_start: 0.6890 (tpt-90) cc_final: 0.6309 (ttm110) REVERT: C 305 PHE cc_start: 0.6853 (p90) cc_final: 0.6362 (p90) REVERT: C 404 HIS cc_start: 0.7355 (m90) cc_final: 0.6804 (m90) REVERT: D 186 SER cc_start: 0.8207 (m) cc_final: 0.7749 (p) REVERT: D 216 PHE cc_start: 0.7462 (m-80) cc_final: 0.6582 (m-80) REVERT: D 270 TYR cc_start: 0.7414 (m-80) cc_final: 0.6993 (m-80) REVERT: D 283 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 286 ARG cc_start: 0.6891 (tpt-90) cc_final: 0.6306 (ttm110) REVERT: D 305 PHE cc_start: 0.6830 (p90) cc_final: 0.6422 (p90) REVERT: D 404 HIS cc_start: 0.7351 (m90) cc_final: 0.6798 (m90) outliers start: 67 outliers final: 46 residues processed: 341 average time/residue: 0.0970 time to fit residues: 51.5829 Evaluate side-chains 336 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 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 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 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 262 LEU 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 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 262 LEU 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 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4309 r_free = 0.4309 target = 0.166482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132277 restraints weight = 16347.872| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.47 r_work: 0.3891 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13772 Z= 0.173 Angle : 0.752 13.583 18776 Z= 0.371 Chirality : 0.051 0.453 2104 Planarity : 0.004 0.057 2344 Dihedral : 5.036 25.326 1820 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.59 % Allowed : 21.52 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.02 (0.21), residues: 1644 helix: -0.39 (0.19), residues: 728 sheet: -0.69 (0.39), residues: 176 loop : -2.51 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 518 TYR 0.026 0.002 TYR C 526 PHE 0.022 0.002 PHE C 305 TRP 0.015 0.002 TRP C 434 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (13768) covalent geometry : angle 0.72633 / 0.37 (18764) hydrogen bonds : bond 0.03409 / 2.25 ( 544) hydrogen bonds : angle 5.20201 / 3.60 ( 1608) link_NAG-ASN : bond 0.00865 / 0.43 ( 4) link_NAG-ASN : angle 7.72214 / 4.75 ( 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 348 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 0.512 Fit side-chains REVERT: A 186 SER cc_start: 0.8229 (m) cc_final: 0.7779 (p) REVERT: A 216 PHE cc_start: 0.7526 (m-80) cc_final: 0.7075 (m-80) REVERT: A 270 TYR cc_start: 0.7674 (m-80) cc_final: 0.7225 (m-80) REVERT: A 283 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 286 ARG cc_start: 0.6932 (tpt-90) cc_final: 0.6336 (ttm110) REVERT: A 404 HIS cc_start: 0.7455 (m90) cc_final: 0.6839 (m90) REVERT: A 527 ASN cc_start: 0.7108 (t0) cc_final: 0.6790 (t0) REVERT: B 186 SER cc_start: 0.8169 (m) cc_final: 0.7724 (p) REVERT: B 216 PHE cc_start: 0.7530 (m-80) cc_final: 0.7079 (m-80) REVERT: B 270 TYR cc_start: 0.7680 (m-80) cc_final: 0.7196 (m-80) REVERT: B 283 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 286 ARG cc_start: 0.6930 (tpt-90) cc_final: 0.6330 (ttm110) REVERT: B 404 HIS cc_start: 0.7454 (m90) cc_final: 0.6838 (m90) REVERT: C 186 SER cc_start: 0.8195 (m) cc_final: 0.7751 (p) REVERT: C 216 PHE cc_start: 0.7443 (m-80) cc_final: 0.6946 (m-80) REVERT: C 270 TYR cc_start: 0.7670 (m-80) cc_final: 0.7193 (m-80) REVERT: C 283 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7978 (mt-10) REVERT: C 286 ARG cc_start: 0.6927 (tpt-90) cc_final: 0.6334 (ttm110) REVERT: C 404 HIS cc_start: 0.7452 (m90) cc_final: 0.6835 (m90) REVERT: C 527 ASN cc_start: 0.7096 (t0) cc_final: 0.6779 (t0) REVERT: D 186 SER cc_start: 0.8171 (m) cc_final: 0.7727 (p) REVERT: D 216 PHE cc_start: 0.7448 (m-80) cc_final: 0.6955 (m-80) REVERT: D 270 TYR cc_start: 0.7670 (m-80) cc_final: 0.7193 (m-80) REVERT: D 283 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 286 ARG cc_start: 0.6934 (tpt-90) cc_final: 0.6337 (ttm110) REVERT: D 404 HIS cc_start: 0.7455 (m90) cc_final: 0.6840 (m90) outliers start: 62 outliers final: 50 residues processed: 316 average time/residue: 0.0951 time to fit residues: 47.6514 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 : 0.547 ------------------------------------------------------------------------------- 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 262 LEU 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 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 262 LEU 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 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 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 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 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 487 VAL Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** D 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 = 0.4294 r_free = 0.4294 target = 0.166017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132019 restraints weight = 16393.055| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.47 r_work: 0.3895 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3353 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= 0.170 Angle : 0.736 12.375 18776 Z= 0.367 Chirality : 0.051 0.447 2104 Planarity : 0.004 0.053 2344 Dihedral : 5.095 29.418 1820 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.10 % Allowed : 20.56 % Favored : 74.33 % 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: -1.93 (0.21), residues: 1644 helix: -0.32 (0.19), residues: 724 sheet: -0.62 (0.40), residues: 176 loop : -2.46 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.023 0.002 TYR A 526 PHE 0.016 0.002 PHE B 506 TRP 0.016 0.002 TRP C 434 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (13768) covalent geometry : angle 0.71033 / 0.36 (18764) hydrogen bonds : bond 0.03453 / 2.28 ( 544) hydrogen bonds : angle 5.24099 / 3.63 ( 1608) link_NAG-ASN : bond 0.00888 / 0.44 ( 4) link_NAG-ASN : angle 7.65119 / 4.70 ( 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 344 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 275 time to evaluate : 0.475 Fit side-chains REVERT: A 186 SER cc_start: 0.8157 (m) cc_final: 0.7710 (p) REVERT: A 216 PHE cc_start: 0.7516 (m-80) cc_final: 0.7088 (m-80) REVERT: A 270 TYR cc_start: 0.7623 (m-80) cc_final: 0.7243 (m-80) REVERT: A 286 ARG cc_start: 0.6939 (tpt-90) cc_final: 0.6323 (ttm110) REVERT: A 296 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5683 (mpt-90) REVERT: A 404 HIS cc_start: 0.7435 (m90) cc_final: 0.6812 (m90) REVERT: A 485 PHE cc_start: 0.7751 (m-80) cc_final: 0.7193 (m-80) REVERT: A 526 TYR cc_start: 0.6602 (t80) cc_final: 0.6293 (t80) REVERT: B 186 SER cc_start: 0.8117 (m) cc_final: 0.7660 (p) REVERT: B 216 PHE cc_start: 0.7512 (m-80) cc_final: 0.7080 (m-80) REVERT: B 270 TYR cc_start: 0.7628 (m-80) cc_final: 0.7216 (m-80) REVERT: B 286 ARG cc_start: 0.6936 (tpt-90) cc_final: 0.6315 (ttm110) REVERT: B 296 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5677 (mpt-90) REVERT: B 404 HIS cc_start: 0.7419 (m90) cc_final: 0.6793 (m90) REVERT: B 485 PHE cc_start: 0.7753 (m-80) cc_final: 0.7192 (m-80) REVERT: B 526 TYR cc_start: 0.6605 (t80) cc_final: 0.6295 (t80) REVERT: C 186 SER cc_start: 0.8022 (m) cc_final: 0.7575 (p) REVERT: C 216 PHE cc_start: 0.7425 (m-80) cc_final: 0.6953 (m-80) REVERT: C 270 TYR cc_start: 0.7617 (m-80) cc_final: 0.7204 (m-80) REVERT: C 286 ARG cc_start: 0.6939 (tpt-90) cc_final: 0.6323 (ttm110) REVERT: C 296 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5693 (mpt-90) REVERT: C 404 HIS cc_start: 0.7434 (m90) cc_final: 0.6819 (m90) REVERT: C 485 PHE cc_start: 0.7755 (m-80) cc_final: 0.7195 (m-80) REVERT: C 526 TYR cc_start: 0.6592 (t80) cc_final: 0.6275 (t80) REVERT: C 527 ASN cc_start: 0.6939 (t0) cc_final: 0.6676 (t0) REVERT: D 186 SER cc_start: 0.8118 (m) cc_final: 0.7667 (p) REVERT: D 216 PHE cc_start: 0.7430 (m-80) cc_final: 0.6964 (m-80) REVERT: D 270 TYR cc_start: 0.7627 (m-80) cc_final: 0.7214 (m-80) REVERT: D 286 ARG cc_start: 0.6954 (tpt-90) cc_final: 0.6333 (ttm110) REVERT: D 296 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5691 (mpt-90) REVERT: D 404 HIS cc_start: 0.7428 (m90) cc_final: 0.6803 (m90) REVERT: D 485 PHE cc_start: 0.7751 (m-80) cc_final: 0.7192 (m-80) REVERT: D 526 TYR cc_start: 0.6599 (t80) cc_final: 0.6289 (t80) outliers start: 69 outliers final: 48 residues processed: 312 average time/residue: 0.1022 time to fit residues: 48.9429 Evaluate side-chains 326 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 262 LEU 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 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 262 LEU 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 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 262 LEU 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 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 262 LEU 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 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.0010 chunk 166 optimal weight: 3.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4315 r_free = 0.4315 target = 0.167583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133422 restraints weight = 16443.094| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.49 r_work: 0.3897 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13772 Z= 0.143 Angle : 0.757 14.143 18776 Z= 0.364 Chirality : 0.050 0.437 2104 Planarity : 0.004 0.055 2344 Dihedral : 4.900 29.396 1820 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.51 % Allowed : 21.38 % 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: -1.82 (0.21), residues: 1644 helix: -0.20 (0.19), residues: 728 sheet: -0.48 (0.40), residues: 176 loop : -2.46 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.019 0.002 TYR D 526 PHE 0.033 0.002 PHE A 305 TRP 0.015 0.001 TRP C 434 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13768) covalent geometry : angle 0.73393 / 0.36 (18764) hydrogen bonds : bond 0.03343 / 2.22 ( 544) hydrogen bonds : angle 5.22018 / 3.61 ( 1608) link_NAG-ASN : bond 0.00990 / 0.50 ( 4) link_NAG-ASN : angle 7.44866 / 4.58 ( 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 345 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 284 time to evaluate : 0.491 Fit side-chains REVERT: A 186 SER cc_start: 0.8032 (m) cc_final: 0.7596 (p) REVERT: A 216 PHE cc_start: 0.7405 (m-80) cc_final: 0.6974 (m-80) REVERT: A 270 TYR cc_start: 0.7632 (m-80) cc_final: 0.7075 (m-80) REVERT: A 283 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 286 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6305 (ttm110) REVERT: A 296 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5677 (mpt-90) REVERT: A 404 HIS cc_start: 0.7359 (m90) cc_final: 0.6770 (m90) REVERT: A 418 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 485 PHE cc_start: 0.7746 (m-80) cc_final: 0.7177 (m-80) REVERT: B 186 SER cc_start: 0.8022 (m) cc_final: 0.7583 (p) REVERT: B 216 PHE cc_start: 0.7404 (m-80) cc_final: 0.6968 (m-80) REVERT: B 270 TYR cc_start: 0.7634 (m-80) cc_final: 0.7081 (m-80) REVERT: B 286 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6303 (ttm110) REVERT: B 296 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5682 (mpt-90) REVERT: B 404 HIS cc_start: 0.7366 (m90) cc_final: 0.6745 (m90) REVERT: B 418 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7216 (mt) REVERT: B 435 GLN cc_start: 0.7574 (tp40) cc_final: 0.7319 (tp40) REVERT: B 485 PHE cc_start: 0.7747 (m-80) cc_final: 0.7176 (m-80) REVERT: C 186 SER cc_start: 0.8043 (m) cc_final: 0.7606 (p) REVERT: C 216 PHE cc_start: 0.7225 (m-80) cc_final: 0.6720 (m-80) REVERT: C 270 TYR cc_start: 0.7627 (m-80) cc_final: 0.7073 (m-80) REVERT: C 283 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7897 (mt-10) REVERT: C 286 ARG cc_start: 0.6921 (tpt-90) cc_final: 0.6302 (ttm110) REVERT: C 296 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5690 (mpt-90) REVERT: C 404 HIS cc_start: 0.7367 (m90) cc_final: 0.6748 (m90) REVERT: C 418 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7217 (mt) REVERT: C 485 PHE cc_start: 0.7751 (m-80) cc_final: 0.7182 (m-80) REVERT: C 503 VAL cc_start: 0.4062 (OUTLIER) cc_final: 0.3827 (p) REVERT: D 186 SER cc_start: 0.8024 (m) cc_final: 0.7592 (p) REVERT: D 216 PHE cc_start: 0.7233 (m-80) cc_final: 0.6733 (m-80) REVERT: D 270 TYR cc_start: 0.7633 (m-80) cc_final: 0.7082 (m-80) REVERT: D 283 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7906 (mt-10) REVERT: D 286 ARG cc_start: 0.6951 (tpt-90) cc_final: 0.6322 (ttm110) REVERT: D 296 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5706 (mpt-90) REVERT: D 404 HIS cc_start: 0.7372 (m90) cc_final: 0.6749 (m90) REVERT: D 435 GLN cc_start: 0.7576 (tp40) cc_final: 0.7320 (tp40) REVERT: D 485 PHE cc_start: 0.7751 (m-80) cc_final: 0.7182 (m-80) REVERT: D 503 VAL cc_start: 0.4044 (OUTLIER) cc_final: 0.3798 (p) outliers start: 61 outliers final: 44 residues processed: 320 average time/residue: 0.1022 time to fit residues: 50.2661 Evaluate side-chains 319 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 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 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 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 262 LEU 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 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 262 LEU 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 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 66 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 132 optimal weight: 0.0370 chunk 145 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 162 optimal weight: 0.0170 chunk 56 optimal weight: 0.0370 chunk 105 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.177276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.142664 restraints weight = 15926.749| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.56 r_work: 0.4082 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13772 Z= 0.117 Angle : 0.714 14.771 18776 Z= 0.347 Chirality : 0.048 0.405 2104 Planarity : 0.004 0.046 2344 Dihedral : 4.545 27.897 1820 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.37 % Allowed : 23.59 % Favored : 74.04 % 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: -1.59 (0.21), residues: 1644 helix: -0.02 (0.19), residues: 740 sheet: -0.36 (0.40), residues: 176 loop : -2.37 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 199 TYR 0.012 0.002 TYR B 526 PHE 0.032 0.001 PHE C 305 TRP 0.014 0.001 TRP D 434 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (13768) covalent geometry : angle 0.69282 / 0.34 (18764) hydrogen bonds : bond 0.03335 / 2.24 ( 544) hydrogen bonds : angle 5.01197 / 3.45 ( 1608) link_NAG-ASN : bond 0.01184 / 0.59 ( 4) link_NAG-ASN : angle 6.84920 / 4.22 ( 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 328 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.559 Fit side-chains REVERT: A 216 PHE cc_start: 0.7414 (m-80) cc_final: 0.7002 (m-80) REVERT: A 286 ARG cc_start: 0.6857 (tpt-90) cc_final: 0.6291 (ttm110) REVERT: A 404 HIS cc_start: 0.7159 (m90) cc_final: 0.6549 (m90) REVERT: A 418 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7264 (mt) REVERT: A 435 GLN cc_start: 0.7558 (tp40) cc_final: 0.7308 (tp40) REVERT: A 485 PHE cc_start: 0.7803 (m-80) cc_final: 0.7242 (m-80) REVERT: B 216 PHE cc_start: 0.7410 (m-80) cc_final: 0.6998 (m-80) REVERT: B 283 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7500 (mp0) REVERT: B 286 ARG cc_start: 0.6873 (tpt-90) cc_final: 0.6303 (ttm110) REVERT: B 404 HIS cc_start: 0.7168 (m90) cc_final: 0.6541 (m90) REVERT: B 418 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7274 (mt) REVERT: B 435 GLN cc_start: 0.7553 (tp40) cc_final: 0.7305 (tp40) REVERT: B 485 PHE cc_start: 0.7800 (m-80) cc_final: 0.7242 (m-80) REVERT: C 216 PHE cc_start: 0.7199 (m-80) cc_final: 0.6376 (m-80) REVERT: C 286 ARG cc_start: 0.6869 (tpt-90) cc_final: 0.6306 (ttm110) REVERT: C 404 HIS cc_start: 0.7204 (m90) cc_final: 0.6572 (m90) REVERT: C 418 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7257 (mt) REVERT: C 435 GLN cc_start: 0.7559 (tp40) cc_final: 0.7309 (tp40) REVERT: C 485 PHE cc_start: 0.7809 (m-80) cc_final: 0.7247 (m-80) REVERT: D 216 PHE cc_start: 0.7211 (m-80) cc_final: 0.6395 (m-80) REVERT: D 286 ARG cc_start: 0.6910 (tpt-90) cc_final: 0.6347 (ttm110) REVERT: D 404 HIS cc_start: 0.7164 (m90) cc_final: 0.6538 (m90) REVERT: D 418 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7272 (mt) REVERT: D 435 GLN cc_start: 0.7554 (tp40) cc_final: 0.7304 (tp40) REVERT: D 485 PHE cc_start: 0.7807 (m-80) cc_final: 0.7248 (m-80) outliers start: 32 outliers final: 12 residues processed: 316 average time/residue: 0.1055 time to fit residues: 50.9800 Evaluate side-chains 294 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 221 LEU 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 331 ILE 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 331 ILE Chi-restraints excluded: chain D residue 418 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 38 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 119 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.180755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.145580 restraints weight = 15982.493| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.70 r_work: 0.3941 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13772 Z= 0.147 Angle : 0.775 15.434 18776 Z= 0.371 Chirality : 0.050 0.403 2104 Planarity : 0.005 0.056 2344 Dihedral : 4.647 25.783 1820 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.78 % Allowed : 25.22 % Favored : 73.00 % 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: -1.59 (0.21), residues: 1644 helix: -0.02 (0.20), residues: 728 sheet: -0.43 (0.40), residues: 176 loop : -2.31 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.040 0.002 TYR C 128 PHE 0.036 0.002 PHE B 305 TRP 0.012 0.001 TRP D 434 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13768) covalent geometry : angle 0.75567 / 0.37 (18764) hydrogen bonds : bond 0.03368 / 2.24 ( 544) hydrogen bonds : angle 5.13433 / 3.52 ( 1608) link_NAG-ASN : bond 0.01023 / 0.51 ( 4) link_NAG-ASN : angle 6.80135 / 4.19 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4557.67 seconds wall clock time: 78 minutes 29.75 seconds (4709.75 seconds total)