Starting phenix.real_space_refine on Thu Jul 31 13:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6du8_8912/07_2025/6du8_8912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6du8_8912/07_2025/6du8_8912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6du8_8912/07_2025/6du8_8912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6du8_8912/07_2025/6du8_8912.map" model { file = "/net/cci-nas-00/data/ceres_data/6du8_8912/07_2025/6du8_8912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6du8_8912/07_2025/6du8_8912.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 7.87, per 1000 atoms: 0.59 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: 4.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.18 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: 4.21 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3312 1.33 - 1.45: 3260 1.45 - 1.57: 7132 1.57 - 1.69: 4 1.69 - 1.81: 60 Bond restraints: 13768 Sorted by residual: bond pdb=" CA GLY B 500 " pdb=" C GLY B 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY A 500 " pdb=" C GLY A 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY D 500 " pdb=" C GLY D 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY C 500 " pdb=" C GLY C 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " ideal model delta sigma weight residual 1.532 1.570 -0.038 1.57e-02 4.06e+03 6.01e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 18128 2.73 - 5.47: 524 5.47 - 8.20: 96 8.20 - 10.93: 8 10.93 - 13.67: 8 Bond angle restraints: 18764 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS A 340 " pdb=" CA LYS A 340 " pdb=" C LYS A 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS C 340 " pdb=" CA LYS C 340 " pdb=" C LYS C 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS D 340 " pdb=" CA LYS D 340 " pdb=" C LYS D 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N GLY C 500 " pdb=" CA GLY C 500 " pdb=" C GLY C 500 " ideal model delta sigma weight residual 110.21 102.15 8.06 9.10e-01 1.21e+00 7.84e+01 ... (remaining 18759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 7084 15.72 - 31.43: 532 31.43 - 47.14: 120 47.14 - 62.86: 8 62.86 - 78.57: 12 Dihedral angle restraints: 7756 sinusoidal: 2848 harmonic: 4908 Sorted by residual: dihedral pdb=" CA TYR C 189 " pdb=" C TYR C 189 " pdb=" N TYR C 190 " pdb=" CA TYR C 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR A 189 " pdb=" C TYR A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR B 189 " pdb=" C TYR B 189 " pdb=" N TYR B 190 " pdb=" CA TYR B 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2080 0.185 - 0.370: 20 0.370 - 0.555: 0 0.555 - 0.740: 0 0.740 - 0.924: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" C1 NAG D 901 " pdb=" ND2 ASN D 207 " pdb=" C2 NAG D 901 " pdb=" O5 NAG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 207 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 207 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 ... (remaining 2101 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 207 " 0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN C 207 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN C 207 " 0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN C 207 " -0.536 2.00e-02 2.50e+03 pdb=" C1 NAG C 901 " 0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 207 " -0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN D 207 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN D 207 " -0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN D 207 " 0.536 2.00e-02 2.50e+03 pdb=" C1 NAG D 901 " -0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 207 " 0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN A 207 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN A 207 " 0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN A 207 " -0.536 2.00e-02 2.50e+03 pdb=" C1 NAG A 901 " 0.364 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 128 2.62 - 3.19: 11312 3.19 - 3.76: 20708 3.76 - 4.33: 26952 4.33 - 4.90: 44754 Nonbonded interactions: 103854 Sorted by model distance: nonbonded pdb=" CB PHE A 315 " pdb=" CD2 LEU A 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE C 315 " pdb=" CD2 LEU C 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE D 315 " pdb=" CD2 LEU D 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE B 315 " pdb=" CD2 LEU B 341 " model vdw 2.046 3.860 nonbonded pdb=" OD1 ASN C 505 " pdb=" OG1 THR C 515 " model vdw 2.218 3.040 ... (remaining 103849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 16.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.110 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13772 Z= 0.327 Angle : 1.450 49.708 18776 Z= 0.708 Chirality : 0.077 0.924 2104 Planarity : 0.007 0.067 2344 Dihedral : 12.525 78.570 4604 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.89 % Allowed : 5.62 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (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 TRP 0.032 0.003 TRP C 259 HIS 0.007 0.003 HIS A 258 PHE 0.032 0.003 PHE D 305 TYR 0.054 0.005 TYR C 129 ARG 0.008 0.001 ARG C 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 4) link_NAG-ASN : angle 35.38520 ( 12) hydrogen bonds : bond 0.14099 ( 544) hydrogen bonds : angle 7.56606 ( 1608) covalent geometry : bond 0.00726 (13768) covalent geometry : angle 1.14155 (18764) *********************** 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 : 1.724 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 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 415 MET cc_start: 0.8328 (mpp) cc_final: 0.8105 (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 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 415 MET cc_start: 0.8327 (mpp) cc_final: 0.8105 (mmp) REVERT: D 435 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6752 (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: 0.2355 time to fit residues: 149.8518 Evaluate side-chains 324 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 312 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 141 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN A 440 ASN A 502 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 440 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 502 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN D 440 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.176155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.140806 restraints weight = 16012.614| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.64 r_work: 0.3970 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13772 Z= 0.136 Angle : 0.722 16.526 18776 Z= 0.366 Chirality : 0.052 0.543 2104 Planarity : 0.005 0.063 2344 Dihedral : 6.716 49.687 1924 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.96 % Allowed : 11.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.18), residues: 1644 helix: -1.92 (0.16), residues: 764 sheet: -1.03 (0.40), residues: 176 loop : -3.14 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 434 HIS 0.004 0.001 HIS C 258 PHE 0.016 0.001 PHE B 556 TYR 0.016 0.002 TYR A 227 ARG 0.003 0.000 ARG B 296 Details of bonding type rmsd link_NAG-ASN : bond 0.01431 ( 4) link_NAG-ASN : angle 10.36427 ( 12) hydrogen bonds : bond 0.03887 ( 544) hydrogen bonds : angle 5.68191 ( 1608) covalent geometry : bond 0.00298 (13768) covalent geometry : angle 0.67299 (18764) *********************** 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 396 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 356 time to evaluate : 1.532 Fit side-chains REVERT: A 133 MET cc_start: 0.6561 (mmp) cc_final: 0.5954 (mmp) REVERT: A 186 SER cc_start: 0.8164 (m) cc_final: 0.7654 (p) REVERT: A 286 ARG cc_start: 0.6809 (tpt-90) cc_final: 0.6506 (ttp-170) REVERT: A 305 PHE cc_start: 0.6948 (p90) cc_final: 0.6333 (p90) REVERT: A 404 HIS cc_start: 0.7575 (m90) cc_final: 0.7159 (m90) REVERT: A 406 PHE cc_start: 0.8285 (t80) cc_final: 0.8015 (t80) REVERT: A 412 ASN cc_start: 0.7936 (m-40) cc_final: 0.7599 (t0) REVERT: A 527 ASN cc_start: 0.6716 (t0) cc_final: 0.6415 (t0) REVERT: B 133 MET cc_start: 0.6542 (mmp) cc_final: 0.5936 (mmp) REVERT: B 186 SER cc_start: 0.8165 (m) cc_final: 0.7650 (p) REVERT: B 286 ARG cc_start: 0.6813 (tpt-90) cc_final: 0.6508 (ttp-170) REVERT: B 305 PHE cc_start: 0.6952 (p90) cc_final: 0.6333 (p90) REVERT: B 404 HIS cc_start: 0.7570 (m90) cc_final: 0.7151 (m90) REVERT: B 406 PHE cc_start: 0.8280 (t80) cc_final: 0.8012 (t80) REVERT: B 412 ASN cc_start: 0.7938 (m-40) cc_final: 0.7595 (t0) REVERT: B 527 ASN cc_start: 0.6707 (t0) cc_final: 0.6407 (t0) REVERT: C 133 MET cc_start: 0.6579 (mmp) cc_final: 0.5966 (mmp) REVERT: C 186 SER cc_start: 0.8170 (m) cc_final: 0.7665 (p) REVERT: C 286 ARG cc_start: 0.6819 (tpt-90) cc_final: 0.6515 (ttp-170) REVERT: C 305 PHE cc_start: 0.6961 (p90) cc_final: 0.6334 (p90) REVERT: C 404 HIS cc_start: 0.7572 (m90) cc_final: 0.7158 (m90) REVERT: C 406 PHE cc_start: 0.8285 (t80) cc_final: 0.8016 (t80) REVERT: C 412 ASN cc_start: 0.7937 (m-40) cc_final: 0.7599 (t0) REVERT: C 527 ASN cc_start: 0.6699 (t0) cc_final: 0.6400 (t0) REVERT: D 133 MET cc_start: 0.6543 (mmp) cc_final: 0.5940 (mmp) REVERT: D 186 SER cc_start: 0.8167 (m) cc_final: 0.7659 (p) REVERT: D 286 ARG cc_start: 0.6817 (tpt-90) cc_final: 0.6514 (ttp-170) REVERT: D 305 PHE cc_start: 0.6966 (p90) cc_final: 0.6341 (p90) REVERT: D 404 HIS cc_start: 0.7570 (m90) cc_final: 0.7152 (m90) REVERT: D 406 PHE cc_start: 0.8282 (t80) cc_final: 0.8014 (t80) REVERT: D 412 ASN cc_start: 0.7935 (m-40) cc_final: 0.7597 (t0) REVERT: D 527 ASN cc_start: 0.6698 (t0) cc_final: 0.6399 (t0) outliers start: 40 outliers final: 12 residues processed: 380 average time/residue: 0.2944 time to fit residues: 170.4390 Evaluate side-chains 298 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 286 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN D 502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.170585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134338 restraints weight = 16264.113| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.63 r_work: 0.3838 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13772 Z= 0.155 Angle : 0.746 15.063 18776 Z= 0.369 Chirality : 0.053 0.569 2104 Planarity : 0.005 0.061 2344 Dihedral : 5.542 29.260 1904 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.70 % Allowed : 14.28 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1644 helix: -1.07 (0.18), residues: 728 sheet: -0.66 (0.40), residues: 176 loop : -2.88 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 434 HIS 0.004 0.001 HIS A 258 PHE 0.021 0.002 PHE B 433 TYR 0.020 0.002 TYR C 129 ARG 0.004 0.000 ARG B 296 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 4) link_NAG-ASN : angle 9.69849 ( 12) hydrogen bonds : bond 0.03703 ( 544) hydrogen bonds : angle 5.39532 ( 1608) covalent geometry : bond 0.00352 (13768) covalent geometry : angle 0.70427 (18764) *********************** 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 356 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 1.575 Fit side-chains REVERT: A 186 SER cc_start: 0.8239 (m) cc_final: 0.7721 (p) REVERT: A 283 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 286 ARG cc_start: 0.6937 (tpt-90) cc_final: 0.6417 (ttm110) REVERT: A 404 HIS cc_start: 0.7639 (m90) cc_final: 0.7138 (m90) REVERT: A 412 ASN cc_start: 0.8084 (m-40) cc_final: 0.7652 (t0) REVERT: A 527 ASN cc_start: 0.6921 (t0) cc_final: 0.6600 (t0) REVERT: B 133 MET cc_start: 0.6442 (mmp) cc_final: 0.5967 (mmp) REVERT: B 186 SER cc_start: 0.8235 (m) cc_final: 0.7714 (p) REVERT: B 283 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 286 ARG cc_start: 0.6942 (tpt-90) cc_final: 0.6427 (ttm110) REVERT: B 404 HIS cc_start: 0.7634 (m90) cc_final: 0.7134 (m90) REVERT: B 412 ASN cc_start: 0.8084 (m-40) cc_final: 0.7652 (t0) REVERT: B 527 ASN cc_start: 0.6924 (t0) cc_final: 0.6601 (t0) REVERT: C 186 SER cc_start: 0.8234 (m) cc_final: 0.7716 (p) REVERT: C 283 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7904 (mt-10) REVERT: C 286 ARG cc_start: 0.6943 (tpt-90) cc_final: 0.6426 (ttm110) REVERT: C 404 HIS cc_start: 0.7644 (m90) cc_final: 0.7148 (m90) REVERT: C 412 ASN cc_start: 0.8085 (m-40) cc_final: 0.7650 (t0) REVERT: C 527 ASN cc_start: 0.6917 (t0) cc_final: 0.6596 (t0) REVERT: D 133 MET cc_start: 0.6459 (mmp) cc_final: 0.5981 (mmp) REVERT: D 186 SER cc_start: 0.8231 (m) cc_final: 0.7709 (p) REVERT: D 283 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 286 ARG cc_start: 0.6940 (tpt-90) cc_final: 0.6424 (ttm110) REVERT: D 404 HIS cc_start: 0.7631 (m90) cc_final: 0.7133 (m90) REVERT: D 412 ASN cc_start: 0.8088 (m-40) cc_final: 0.7652 (t0) REVERT: D 527 ASN cc_start: 0.6926 (t0) cc_final: 0.6605 (t0) outliers start: 50 outliers final: 28 residues processed: 334 average time/residue: 0.3655 time to fit residues: 192.8175 Evaluate side-chains 324 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 221 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 122 THR Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 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 122 THR Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 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 122 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 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 59 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 192 ASN C 192 ASN C 289 GLN D 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.163484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128712 restraints weight = 16564.727| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.53 r_work: 0.3790 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13772 Z= 0.230 Angle : 0.789 13.893 18776 Z= 0.401 Chirality : 0.055 0.556 2104 Planarity : 0.005 0.062 2344 Dihedral : 6.035 26.657 1904 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 4.66 % Allowed : 15.98 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1644 helix: -0.87 (0.19), residues: 732 sheet: -0.84 (0.41), residues: 176 loop : -2.89 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 434 HIS 0.005 0.001 HIS D 258 PHE 0.033 0.002 PHE B 305 TYR 0.031 0.003 TYR B 526 ARG 0.003 0.000 ARG A 296 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 4) link_NAG-ASN : angle 9.08709 ( 12) hydrogen bonds : bond 0.03718 ( 544) hydrogen bonds : angle 5.43019 ( 1608) covalent geometry : bond 0.00546 (13768) covalent geometry : angle 0.75472 (18764) *********************** 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 357 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 294 time to evaluate : 2.988 Fit side-chains REVERT: A 133 MET cc_start: 0.6434 (mmp) cc_final: 0.6023 (mmp) REVERT: A 186 SER cc_start: 0.8249 (m) cc_final: 0.7770 (p) REVERT: A 270 TYR cc_start: 0.7704 (m-80) cc_final: 0.7219 (m-80) REVERT: A 286 ARG cc_start: 0.6845 (tpt-90) cc_final: 0.6441 (ttp-170) REVERT: A 305 PHE cc_start: 0.6864 (p90) cc_final: 0.6422 (p90) REVERT: A 404 HIS cc_start: 0.7681 (m90) cc_final: 0.7253 (m90) REVERT: A 485 PHE cc_start: 0.7813 (m-80) cc_final: 0.7081 (m-80) REVERT: A 527 ASN cc_start: 0.6958 (t0) cc_final: 0.6638 (t0) REVERT: B 186 SER cc_start: 0.8242 (m) cc_final: 0.7762 (p) REVERT: B 270 TYR cc_start: 0.7700 (m-80) cc_final: 0.7218 (m-80) REVERT: B 286 ARG cc_start: 0.6848 (tpt-90) cc_final: 0.6445 (ttp-170) REVERT: B 305 PHE cc_start: 0.6859 (p90) cc_final: 0.6426 (p90) REVERT: B 404 HIS cc_start: 0.7682 (m90) cc_final: 0.7254 (m90) REVERT: B 485 PHE cc_start: 0.7814 (m-80) cc_final: 0.7071 (m-80) REVERT: B 527 ASN cc_start: 0.6962 (t0) cc_final: 0.6643 (t0) REVERT: C 133 MET cc_start: 0.6473 (mmp) cc_final: 0.6089 (mmt) REVERT: C 186 SER cc_start: 0.8242 (m) cc_final: 0.7764 (p) REVERT: C 270 TYR cc_start: 0.7696 (m-80) cc_final: 0.7208 (m-80) REVERT: C 286 ARG cc_start: 0.6849 (tpt-90) cc_final: 0.6444 (ttp-170) REVERT: C 305 PHE cc_start: 0.6863 (p90) cc_final: 0.6398 (p90) REVERT: C 404 HIS cc_start: 0.7691 (m90) cc_final: 0.7258 (m90) REVERT: C 485 PHE cc_start: 0.7814 (m-80) cc_final: 0.7086 (m-80) REVERT: C 527 ASN cc_start: 0.6946 (t0) cc_final: 0.6626 (t0) REVERT: D 186 SER cc_start: 0.8241 (m) cc_final: 0.7763 (p) REVERT: D 270 TYR cc_start: 0.7698 (m-80) cc_final: 0.7213 (m-80) REVERT: D 286 ARG cc_start: 0.6850 (tpt-90) cc_final: 0.6447 (ttp-170) REVERT: D 305 PHE cc_start: 0.6863 (p90) cc_final: 0.6402 (p90) REVERT: D 404 HIS cc_start: 0.7693 (m90) cc_final: 0.7259 (m90) REVERT: D 485 PHE cc_start: 0.7815 (m-80) cc_final: 0.7079 (m-80) REVERT: D 527 ASN cc_start: 0.6952 (t0) cc_final: 0.6634 (t0) outliers start: 63 outliers final: 40 residues processed: 337 average time/residue: 0.2987 time to fit residues: 156.3932 Evaluate side-chains 320 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 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 230 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain 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 230 ASP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.167190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.132826 restraints weight = 16344.900| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.50 r_work: 0.3924 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.3006 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= 0.142 Angle : 0.714 13.259 18776 Z= 0.354 Chirality : 0.051 0.519 2104 Planarity : 0.004 0.055 2344 Dihedral : 5.511 26.998 1904 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.85 % Allowed : 19.23 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.20), residues: 1644 helix: -0.58 (0.19), residues: 724 sheet: -0.74 (0.40), residues: 176 loop : -2.70 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 434 HIS 0.003 0.001 HIS A 258 PHE 0.027 0.002 PHE A 305 TYR 0.020 0.002 TYR A 526 ARG 0.002 0.000 ARG B 296 Details of bonding type rmsd link_NAG-ASN : bond 0.01108 ( 4) link_NAG-ASN : angle 8.65918 ( 12) hydrogen bonds : bond 0.03364 ( 544) hydrogen bonds : angle 5.30131 ( 1608) covalent geometry : bond 0.00327 (13768) covalent geometry : angle 0.67953 (18764) *********************** 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 356 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 1.392 Fit side-chains REVERT: A 186 SER cc_start: 0.8271 (m) cc_final: 0.7793 (p) REVERT: A 216 PHE cc_start: 0.7404 (m-80) cc_final: 0.6542 (m-80) REVERT: A 270 TYR cc_start: 0.7522 (m-80) cc_final: 0.7100 (m-80) REVERT: A 286 ARG cc_start: 0.6804 (tpt-90) cc_final: 0.6353 (ttm110) REVERT: A 305 PHE cc_start: 0.6950 (p90) cc_final: 0.6477 (p90) REVERT: A 404 HIS cc_start: 0.7369 (m90) cc_final: 0.6940 (m90) REVERT: A 406 PHE cc_start: 0.8253 (t80) cc_final: 0.8005 (t80) REVERT: A 485 PHE cc_start: 0.7809 (m-80) cc_final: 0.7045 (m-80) REVERT: B 186 SER cc_start: 0.8257 (m) cc_final: 0.7775 (p) REVERT: B 216 PHE cc_start: 0.7404 (m-80) cc_final: 0.6536 (m-80) REVERT: B 270 TYR cc_start: 0.7519 (m-80) cc_final: 0.7100 (m-80) REVERT: B 286 ARG cc_start: 0.6808 (tpt-90) cc_final: 0.6352 (ttm110) REVERT: B 305 PHE cc_start: 0.6950 (p90) cc_final: 0.6471 (p90) REVERT: B 404 HIS cc_start: 0.7373 (m90) cc_final: 0.6943 (m90) REVERT: B 406 PHE cc_start: 0.8250 (t80) cc_final: 0.8002 (t80) REVERT: B 485 PHE cc_start: 0.7811 (m-80) cc_final: 0.7043 (m-80) REVERT: C 186 SER cc_start: 0.8253 (m) cc_final: 0.7776 (p) REVERT: C 270 TYR cc_start: 0.7526 (m-80) cc_final: 0.7105 (m-80) REVERT: C 286 ARG cc_start: 0.6802 (tpt-90) cc_final: 0.6349 (ttm110) REVERT: C 305 PHE cc_start: 0.6945 (p90) cc_final: 0.6465 (p90) REVERT: C 404 HIS cc_start: 0.7368 (m90) cc_final: 0.6946 (m90) REVERT: C 406 PHE cc_start: 0.8256 (t80) cc_final: 0.8004 (t80) REVERT: C 485 PHE cc_start: 0.7815 (m-80) cc_final: 0.7050 (m-80) REVERT: D 186 SER cc_start: 0.8259 (m) cc_final: 0.7778 (p) REVERT: D 270 TYR cc_start: 0.7521 (m-80) cc_final: 0.7102 (m-80) REVERT: D 286 ARG cc_start: 0.6807 (tpt-90) cc_final: 0.6355 (ttm110) REVERT: D 305 PHE cc_start: 0.6942 (p90) cc_final: 0.6471 (p90) REVERT: D 404 HIS cc_start: 0.7371 (m90) cc_final: 0.6947 (m90) REVERT: D 406 PHE cc_start: 0.8262 (t80) cc_final: 0.8010 (t80) REVERT: D 485 PHE cc_start: 0.7812 (m-80) cc_final: 0.7046 (m-80) outliers start: 52 outliers final: 38 residues processed: 340 average time/residue: 0.2002 time to fit residues: 104.8425 Evaluate side-chains 331 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 251 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 318 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 197 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 318 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4303 r_free = 0.4303 target = 0.166530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132275 restraints weight = 16645.096| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.50 r_work: 0.3883 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13772 Z= 0.154 Angle : 0.728 13.471 18776 Z= 0.360 Chirality : 0.051 0.503 2104 Planarity : 0.004 0.058 2344 Dihedral : 5.420 28.032 1904 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.36 % Allowed : 20.93 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.20), residues: 1644 helix: -0.50 (0.19), residues: 728 sheet: -0.79 (0.39), residues: 176 loop : -2.64 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 434 HIS 0.003 0.001 HIS A 258 PHE 0.024 0.002 PHE A 305 TYR 0.025 0.002 TYR C 526 ARG 0.002 0.000 ARG B 296 Details of bonding type rmsd link_NAG-ASN : bond 0.01055 ( 4) link_NAG-ASN : angle 8.34126 ( 12) hydrogen bonds : bond 0.03338 ( 544) hydrogen bonds : angle 5.27864 ( 1608) covalent geometry : bond 0.00356 (13768) covalent geometry : angle 0.69665 (18764) *********************** 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 350 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 291 time to evaluate : 1.345 Fit side-chains REVERT: A 186 SER cc_start: 0.8210 (m) cc_final: 0.7759 (p) REVERT: A 216 PHE cc_start: 0.7467 (m-80) cc_final: 0.6993 (m-80) REVERT: A 270 TYR cc_start: 0.7528 (m-80) cc_final: 0.7024 (m-80) REVERT: A 283 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 286 ARG cc_start: 0.6722 (tpt-90) cc_final: 0.6263 (ttm110) REVERT: A 305 PHE cc_start: 0.6894 (p90) cc_final: 0.6434 (p90) REVERT: A 404 HIS cc_start: 0.7327 (m90) cc_final: 0.6703 (m90) REVERT: A 406 PHE cc_start: 0.8208 (t80) cc_final: 0.7999 (t80) REVERT: A 485 PHE cc_start: 0.7836 (m-80) cc_final: 0.7100 (m-80) REVERT: A 503 VAL cc_start: 0.4163 (OUTLIER) cc_final: 0.3947 (p) REVERT: B 186 SER cc_start: 0.8201 (m) cc_final: 0.7747 (p) REVERT: B 216 PHE cc_start: 0.7468 (m-80) cc_final: 0.6987 (m-80) REVERT: B 270 TYR cc_start: 0.7530 (m-80) cc_final: 0.7028 (m-80) REVERT: B 283 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 286 ARG cc_start: 0.6733 (tpt-90) cc_final: 0.6271 (ttm110) REVERT: B 305 PHE cc_start: 0.6895 (p90) cc_final: 0.6430 (p90) REVERT: B 404 HIS cc_start: 0.7330 (m90) cc_final: 0.6709 (m90) REVERT: B 406 PHE cc_start: 0.8208 (t80) cc_final: 0.7990 (t80) REVERT: B 485 PHE cc_start: 0.7811 (m-80) cc_final: 0.7050 (m-80) REVERT: B 503 VAL cc_start: 0.4153 (OUTLIER) cc_final: 0.3936 (p) REVERT: C 186 SER cc_start: 0.8199 (m) cc_final: 0.7745 (p) REVERT: C 216 PHE cc_start: 0.7199 (m-80) cc_final: 0.6893 (m-80) REVERT: C 270 TYR cc_start: 0.7532 (m-80) cc_final: 0.7027 (m-80) REVERT: C 283 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 286 ARG cc_start: 0.6728 (tpt-90) cc_final: 0.6272 (ttm110) REVERT: C 305 PHE cc_start: 0.6898 (p90) cc_final: 0.6437 (p90) REVERT: C 404 HIS cc_start: 0.7399 (m90) cc_final: 0.6876 (m90) REVERT: C 406 PHE cc_start: 0.8209 (t80) cc_final: 0.7992 (t80) REVERT: C 485 PHE cc_start: 0.7784 (m-80) cc_final: 0.7040 (m-80) REVERT: C 503 VAL cc_start: 0.4247 (OUTLIER) cc_final: 0.4026 (p) REVERT: D 186 SER cc_start: 0.8192 (m) cc_final: 0.7740 (p) REVERT: D 216 PHE cc_start: 0.7200 (m-80) cc_final: 0.6893 (m-80) REVERT: D 270 TYR cc_start: 0.7533 (m-80) cc_final: 0.7029 (m-80) REVERT: D 283 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7768 (mt-10) REVERT: D 286 ARG cc_start: 0.6744 (tpt-90) cc_final: 0.6280 (ttm110) REVERT: D 305 PHE cc_start: 0.6884 (p90) cc_final: 0.6426 (p90) REVERT: D 404 HIS cc_start: 0.7397 (m90) cc_final: 0.6874 (m90) REVERT: D 406 PHE cc_start: 0.8212 (t80) cc_final: 0.7993 (t80) REVERT: D 485 PHE cc_start: 0.7822 (m-80) cc_final: 0.7082 (m-80) REVERT: D 503 VAL cc_start: 0.4246 (OUTLIER) cc_final: 0.4025 (p) outliers start: 59 outliers final: 41 residues processed: 330 average time/residue: 0.2275 time to fit residues: 115.6479 Evaluate side-chains 327 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 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 318 LEU 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 318 LEU 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 318 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 137 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.175218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.140032 restraints weight = 16020.040| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.61 r_work: 0.3984 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13772 Z= 0.114 Angle : 0.697 13.494 18776 Z= 0.338 Chirality : 0.049 0.465 2104 Planarity : 0.004 0.049 2344 Dihedral : 4.933 26.983 1904 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.44 % Allowed : 23.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.20), residues: 1644 helix: -0.32 (0.19), residues: 724 sheet: -0.48 (0.40), residues: 176 loop : -2.39 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 434 HIS 0.002 0.001 HIS A 258 PHE 0.023 0.001 PHE A 305 TYR 0.013 0.002 TYR D 308 ARG 0.003 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01276 ( 4) link_NAG-ASN : angle 7.87492 ( 12) hydrogen bonds : bond 0.03194 ( 544) hydrogen bonds : angle 5.06431 ( 1608) covalent geometry : bond 0.00236 (13768) covalent geometry : angle 0.66856 (18764) *********************** 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 342 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 1.529 Fit side-chains REVERT: A 186 SER cc_start: 0.8167 (m) cc_final: 0.7716 (p) REVERT: A 216 PHE cc_start: 0.7270 (m-80) cc_final: 0.6848 (m-80) REVERT: A 283 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 286 ARG cc_start: 0.6738 (tpt-90) cc_final: 0.6281 (ttm110) REVERT: A 305 PHE cc_start: 0.6789 (p90) cc_final: 0.6337 (p90) REVERT: A 404 HIS cc_start: 0.7076 (m90) cc_final: 0.6493 (m90) REVERT: A 406 PHE cc_start: 0.8178 (t80) cc_final: 0.7923 (t80) REVERT: B 186 SER cc_start: 0.8160 (m) cc_final: 0.7703 (p) REVERT: B 216 PHE cc_start: 0.7269 (m-80) cc_final: 0.6845 (m-80) REVERT: B 283 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 286 ARG cc_start: 0.6727 (tpt-90) cc_final: 0.6268 (ttm110) REVERT: B 305 PHE cc_start: 0.6786 (p90) cc_final: 0.6311 (p90) REVERT: B 404 HIS cc_start: 0.7072 (m90) cc_final: 0.6488 (m90) REVERT: C 186 SER cc_start: 0.8154 (m) cc_final: 0.7695 (p) REVERT: C 216 PHE cc_start: 0.7099 (m-80) cc_final: 0.6833 (m-80) REVERT: C 283 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 286 ARG cc_start: 0.6738 (tpt-90) cc_final: 0.6278 (ttm110) REVERT: C 305 PHE cc_start: 0.6792 (p90) cc_final: 0.6320 (p90) REVERT: C 404 HIS cc_start: 0.7058 (m90) cc_final: 0.6531 (m90) REVERT: D 186 SER cc_start: 0.8155 (m) cc_final: 0.7694 (p) REVERT: D 216 PHE cc_start: 0.7107 (m-80) cc_final: 0.6840 (m-80) REVERT: D 283 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 286 ARG cc_start: 0.6743 (tpt-90) cc_final: 0.6283 (ttm110) REVERT: D 305 PHE cc_start: 0.6785 (p90) cc_final: 0.6308 (p90) REVERT: D 404 HIS cc_start: 0.7042 (m90) cc_final: 0.6522 (m90) outliers start: 33 outliers final: 24 residues processed: 322 average time/residue: 0.2074 time to fit residues: 101.8770 Evaluate side-chains 315 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.174667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.139273 restraints weight = 16159.077| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.61 r_work: 0.4023 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13772 Z= 0.118 Angle : 0.707 12.965 18776 Z= 0.341 Chirality : 0.049 0.447 2104 Planarity : 0.004 0.053 2344 Dihedral : 4.804 26.719 1904 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.88 % Allowed : 24.41 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1644 helix: -0.27 (0.19), residues: 732 sheet: -0.43 (0.40), residues: 176 loop : -2.36 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 434 HIS 0.002 0.001 HIS D 258 PHE 0.024 0.002 PHE A 351 TYR 0.023 0.002 TYR D 128 ARG 0.001 0.000 ARG C 413 Details of bonding type rmsd link_NAG-ASN : bond 0.01206 ( 4) link_NAG-ASN : angle 7.35917 ( 12) hydrogen bonds : bond 0.03191 ( 544) hydrogen bonds : angle 5.13502 ( 1608) covalent geometry : bond 0.00256 (13768) covalent geometry : angle 0.68192 (18764) *********************** 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 336 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.459 Fit side-chains REVERT: A 186 SER cc_start: 0.8145 (m) cc_final: 0.7715 (p) REVERT: A 216 PHE cc_start: 0.7239 (m-80) cc_final: 0.6756 (m-80) REVERT: A 270 TYR cc_start: 0.7269 (m-80) cc_final: 0.6938 (m-80) REVERT: A 283 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 286 ARG cc_start: 0.6715 (tpt-90) cc_final: 0.6304 (ttm110) REVERT: A 305 PHE cc_start: 0.6853 (p90) cc_final: 0.6378 (p90) REVERT: A 404 HIS cc_start: 0.7204 (m90) cc_final: 0.6574 (m90) REVERT: A 418 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7162 (mt) REVERT: A 435 GLN cc_start: 0.7575 (tp40) cc_final: 0.7361 (tp40) REVERT: A 446 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7475 (tt) REVERT: B 127 TYR cc_start: 0.6316 (p90) cc_final: 0.5869 (p90) REVERT: B 186 SER cc_start: 0.8143 (m) cc_final: 0.7713 (p) REVERT: B 216 PHE cc_start: 0.7244 (m-80) cc_final: 0.6758 (m-80) REVERT: B 270 TYR cc_start: 0.7267 (m-80) cc_final: 0.6943 (m-80) REVERT: B 283 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 286 ARG cc_start: 0.6710 (tpt-90) cc_final: 0.6296 (ttm110) REVERT: B 305 PHE cc_start: 0.6851 (p90) cc_final: 0.6365 (p90) REVERT: B 404 HIS cc_start: 0.7194 (m90) cc_final: 0.6620 (m90) REVERT: B 418 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7207 (mt) REVERT: B 435 GLN cc_start: 0.7573 (tp40) cc_final: 0.7357 (tp40) REVERT: B 446 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7477 (tt) REVERT: C 186 SER cc_start: 0.8142 (m) cc_final: 0.7707 (p) REVERT: C 216 PHE cc_start: 0.7177 (m-80) cc_final: 0.6877 (m-80) REVERT: C 270 TYR cc_start: 0.7275 (m-80) cc_final: 0.6946 (m-80) REVERT: C 283 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7809 (mt-10) REVERT: C 286 ARG cc_start: 0.6717 (tpt-90) cc_final: 0.6301 (ttm110) REVERT: C 305 PHE cc_start: 0.6844 (p90) cc_final: 0.6369 (p90) REVERT: C 404 HIS cc_start: 0.7229 (m90) cc_final: 0.6616 (m90) REVERT: C 418 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7168 (mt) REVERT: C 435 GLN cc_start: 0.7642 (tp40) cc_final: 0.7425 (tp40) REVERT: D 127 TYR cc_start: 0.6316 (p90) cc_final: 0.5846 (p90) REVERT: D 186 SER cc_start: 0.8134 (m) cc_final: 0.7705 (p) REVERT: D 216 PHE cc_start: 0.7186 (m-80) cc_final: 0.6888 (m-80) REVERT: D 270 TYR cc_start: 0.7270 (m-80) cc_final: 0.6947 (m-80) REVERT: D 283 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7809 (mt-10) REVERT: D 286 ARG cc_start: 0.6724 (tpt-90) cc_final: 0.6307 (ttm110) REVERT: D 305 PHE cc_start: 0.6845 (p90) cc_final: 0.6363 (p90) REVERT: D 404 HIS cc_start: 0.7220 (m90) cc_final: 0.6607 (m90) REVERT: D 418 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7207 (mt) REVERT: D 435 GLN cc_start: 0.7649 (tp40) cc_final: 0.7428 (tp40) REVERT: D 446 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7469 (tt) outliers start: 39 outliers final: 24 residues processed: 316 average time/residue: 0.2035 time to fit residues: 99.3327 Evaluate side-chains 307 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 510 ILE 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 336 ILE 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 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.141817 restraints weight = 15926.948| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 3.59 r_work: 0.4063 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.3777 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= 0.114 Angle : 0.724 15.094 18776 Z= 0.340 Chirality : 0.048 0.426 2104 Planarity : 0.004 0.049 2344 Dihedral : 4.633 24.208 1904 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.92 % Allowed : 26.04 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1644 helix: -0.14 (0.19), residues: 732 sheet: -0.30 (0.41), residues: 176 loop : -2.29 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 434 HIS 0.002 0.001 HIS D 258 PHE 0.022 0.001 PHE A 305 TYR 0.015 0.002 TYR B 128 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01254 ( 4) link_NAG-ASN : angle 7.02827 ( 12) hydrogen bonds : bond 0.03173 ( 544) hydrogen bonds : angle 5.05503 ( 1608) covalent geometry : bond 0.00241 (13768) covalent geometry : angle 0.70168 (18764) *********************** 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 310 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 1.363 Fit side-chains REVERT: A 216 PHE cc_start: 0.7224 (m-80) cc_final: 0.6406 (m-80) REVERT: A 283 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 286 ARG cc_start: 0.6708 (tpt-90) cc_final: 0.6267 (ttm110) REVERT: A 305 PHE cc_start: 0.6861 (p90) cc_final: 0.6428 (p90) REVERT: A 404 HIS cc_start: 0.7211 (m90) cc_final: 0.6554 (m90) REVERT: A 418 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7235 (mt) REVERT: A 435 GLN cc_start: 0.7587 (tp40) cc_final: 0.7355 (tp40) REVERT: B 216 PHE cc_start: 0.7225 (m-80) cc_final: 0.6393 (m-80) REVERT: B 283 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 286 ARG cc_start: 0.6721 (tpt-90) cc_final: 0.6288 (ttm110) REVERT: B 305 PHE cc_start: 0.6854 (p90) cc_final: 0.6423 (p90) REVERT: B 404 HIS cc_start: 0.7213 (m90) cc_final: 0.6594 (m90) REVERT: B 418 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7234 (mt) REVERT: B 435 GLN cc_start: 0.7585 (tp40) cc_final: 0.7339 (tp40) REVERT: C 216 PHE cc_start: 0.7321 (m-80) cc_final: 0.6947 (m-80) REVERT: C 283 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 286 ARG cc_start: 0.6710 (tpt-90) cc_final: 0.6268 (ttm110) REVERT: C 305 PHE cc_start: 0.6863 (p90) cc_final: 0.6439 (p90) REVERT: C 404 HIS cc_start: 0.7212 (m90) cc_final: 0.6577 (m90) REVERT: C 418 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7239 (mt) REVERT: C 435 GLN cc_start: 0.7637 (tp40) cc_final: 0.7395 (tp40) REVERT: D 216 PHE cc_start: 0.7230 (m-80) cc_final: 0.6913 (m-80) REVERT: D 232 GLU cc_start: 0.8939 (mp0) cc_final: 0.8683 (mp0) REVERT: D 283 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7820 (mt-10) REVERT: D 286 ARG cc_start: 0.6724 (tpt-90) cc_final: 0.6278 (ttm110) REVERT: D 305 PHE cc_start: 0.6863 (p90) cc_final: 0.6434 (p90) REVERT: D 404 HIS cc_start: 0.7218 (m90) cc_final: 0.6585 (m90) REVERT: D 418 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7238 (mt) REVERT: D 435 GLN cc_start: 0.7595 (tp40) cc_final: 0.7353 (tp40) outliers start: 26 outliers final: 22 residues processed: 294 average time/residue: 0.2004 time to fit residues: 92.3832 Evaluate side-chains 301 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 487 VAL 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 336 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.174240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.139040 restraints weight = 16144.910| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.59 r_work: 0.3967 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13772 Z= 0.125 Angle : 0.719 15.467 18776 Z= 0.346 Chirality : 0.048 0.421 2104 Planarity : 0.004 0.052 2344 Dihedral : 4.626 23.033 1904 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.22 % Allowed : 26.04 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.21), residues: 1644 helix: -0.12 (0.19), residues: 732 sheet: -0.26 (0.41), residues: 176 loop : -2.27 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 434 HIS 0.002 0.001 HIS D 258 PHE 0.021 0.001 PHE A 305 TYR 0.018 0.002 TYR A 496 ARG 0.002 0.000 ARG C 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01167 ( 4) link_NAG-ASN : angle 6.90535 ( 12) hydrogen bonds : bond 0.03172 ( 544) hydrogen bonds : angle 5.07720 ( 1608) covalent geometry : bond 0.00276 (13768) covalent geometry : angle 0.69783 (18764) ********************** 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 316 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 1.307 Fit side-chains REVERT: A 216 PHE cc_start: 0.7265 (m-80) cc_final: 0.6441 (m-80) REVERT: A 270 TYR cc_start: 0.7311 (m-80) cc_final: 0.6897 (m-80) REVERT: A 286 ARG cc_start: 0.6719 (tpt-90) cc_final: 0.6354 (ttp-170) REVERT: A 305 PHE cc_start: 0.6883 (p90) cc_final: 0.6537 (p90) REVERT: A 404 HIS cc_start: 0.7294 (m90) cc_final: 0.6621 (m90) REVERT: A 435 GLN cc_start: 0.7608 (tp40) cc_final: 0.7365 (tp40) REVERT: A 527 ASN cc_start: 0.6892 (t0) cc_final: 0.6650 (t0) REVERT: B 216 PHE cc_start: 0.7245 (m-80) cc_final: 0.6406 (m-80) REVERT: B 270 TYR cc_start: 0.7314 (m-80) cc_final: 0.6901 (m-80) REVERT: B 286 ARG cc_start: 0.6712 (tpt-90) cc_final: 0.6345 (ttp-170) REVERT: B 305 PHE cc_start: 0.6893 (p90) cc_final: 0.6435 (p90) REVERT: B 404 HIS cc_start: 0.7337 (m90) cc_final: 0.6655 (m90) REVERT: B 418 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7247 (mt) REVERT: B 435 GLN cc_start: 0.7597 (tp40) cc_final: 0.7349 (tp40) REVERT: B 527 ASN cc_start: 0.6878 (t0) cc_final: 0.6637 (t0) REVERT: C 216 PHE cc_start: 0.7311 (m-80) cc_final: 0.6911 (m-80) REVERT: C 270 TYR cc_start: 0.7321 (m-80) cc_final: 0.6909 (m-80) REVERT: C 286 ARG cc_start: 0.6724 (tpt-90) cc_final: 0.6359 (ttp-170) REVERT: C 305 PHE cc_start: 0.6897 (p90) cc_final: 0.6448 (p90) REVERT: C 404 HIS cc_start: 0.7330 (m90) cc_final: 0.6662 (m90) REVERT: C 418 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7246 (mt) REVERT: C 435 GLN cc_start: 0.7603 (tp40) cc_final: 0.7358 (tp40) REVERT: D 216 PHE cc_start: 0.7309 (m-80) cc_final: 0.6900 (m-80) REVERT: D 270 TYR cc_start: 0.7319 (m-80) cc_final: 0.6915 (m-80) REVERT: D 286 ARG cc_start: 0.6732 (tpt-90) cc_final: 0.6362 (ttp-170) REVERT: D 305 PHE cc_start: 0.6902 (p90) cc_final: 0.6448 (p90) REVERT: D 404 HIS cc_start: 0.7331 (m90) cc_final: 0.6662 (m90) REVERT: D 418 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7250 (mt) REVERT: D 435 GLN cc_start: 0.7606 (tp40) cc_final: 0.7359 (tp40) REVERT: D 527 ASN cc_start: 0.6882 (t0) cc_final: 0.6638 (t0) outliers start: 30 outliers final: 23 residues processed: 300 average time/residue: 0.1916 time to fit residues: 91.4816 Evaluate side-chains 308 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 487 VAL 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 336 ILE 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 221 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 126 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.173294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138254 restraints weight = 16140.144| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 3.53 r_work: 0.4019 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13772 Z= 0.131 Angle : 0.741 15.211 18776 Z= 0.352 Chirality : 0.048 0.415 2104 Planarity : 0.004 0.054 2344 Dihedral : 4.661 21.870 1904 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.66 % Allowed : 26.41 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1644 helix: -0.08 (0.19), residues: 732 sheet: -0.25 (0.41), residues: 176 loop : -2.30 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 434 HIS 0.003 0.001 HIS D 258 PHE 0.021 0.001 PHE A 305 TYR 0.019 0.002 TYR B 128 ARG 0.001 0.000 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01128 ( 4) link_NAG-ASN : angle 6.79946 ( 12) hydrogen bonds : bond 0.03216 ( 544) hydrogen bonds : angle 5.17436 ( 1608) covalent geometry : bond 0.00292 (13768) covalent geometry : angle 0.72105 (18764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11067.43 seconds wall clock time: 198 minutes 24.50 seconds (11904.50 seconds total)