Starting phenix.real_space_refine on Sun Sep 13 04:36:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvm_20493/09_2026/6pvm_20493.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.247 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: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 2 4.78 5 C 13648 2.51 5 N 3480 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21006 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "B" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.22 Number of scatterers: 21006 At special positions: 0 Unit cell: (162.18, 162.18, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 2 11.00 O 3752 8.00 N 3480 7.00 C 13648 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 872.8 milliseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 58.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.608A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.719A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.644A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.848A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.876A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.903A pdb=" N SER A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.599A pdb=" N GLU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 420' Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.646A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.536A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.777A pdb=" N HIS A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.507A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.540A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.617A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.609A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.720A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.848A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.660A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.877A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.903A pdb=" N SER B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 374' Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.536A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 540 removed outlier: 3.776A pdb=" N HIS B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 581 through 586 removed outlier: 4.506A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.617A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.609A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.720A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.847A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.857A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.877A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.902A pdb=" N SER C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.648A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.998A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.683A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 374' Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.567A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.535A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 removed outlier: 3.776A pdb=" N HIS C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.628A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 581 through 586 removed outlier: 4.506A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.326A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 607 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 685 removed outlier: 3.638A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.616A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.608A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.719A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 172 through 178 removed outlier: 4.123A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.645A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.847A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.669A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.856A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.661A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.876A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.901A pdb=" N SER D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.598A pdb=" N GLU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.649A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.999A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.682A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 374' Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.566A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.647A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.535A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 505 removed outlier: 4.369A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 540 removed outlier: 3.777A pdb=" N HIS D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.629A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.507A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 4.325A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 607 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.539A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 removed outlier: 3.654A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 685 removed outlier: 3.639A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.616A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 387 through 388 736 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6493 1.34 - 1.46: 4374 1.46 - 1.58: 10389 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21460 Sorted by residual: bond pdb=" C LEU A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.391 -0.058 2.34e-02 1.83e+03 6.04e+00 bond pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.96e+00 bond pdb=" C LEU C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.95e+00 bond pdb=" C LEU D 469 " pdb=" N PRO D 470 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.89e+00 bond pdb=" C ARG B 509 " pdb=" N PRO B 510 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.81e+00 ... (remaining 21455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 28142 2.95 - 5.90: 715 5.90 - 8.85: 159 8.85 - 11.80: 12 11.80 - 14.76: 4 Bond angle restraints: 29032 Sorted by residual: angle pdb=" C TRP B 739 " pdb=" N THR B 740 " pdb=" CA THR B 740 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" C TRP C 739 " pdb=" N THR C 740 " pdb=" CA THR C 740 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" C TRP A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C TRP D 739 " pdb=" N THR D 740 " pdb=" CA THR D 740 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" N ILE D 503 " pdb=" CA ILE D 503 " pdb=" C ILE D 503 " ideal model delta sigma weight residual 112.96 107.49 5.47 1.00e+00 1.00e+00 2.99e+01 ... (remaining 29027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 11556 14.98 - 29.97: 935 29.97 - 44.95: 309 44.95 - 59.93: 36 59.93 - 74.91: 20 Dihedral angle restraints: 12856 sinusoidal: 5252 harmonic: 7604 Sorted by residual: dihedral pdb=" CA HIS C 256 " pdb=" C HIS C 256 " pdb=" N GLU C 257 " pdb=" CA GLU C 257 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA HIS B 256 " pdb=" C HIS B 256 " pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA HIS D 256 " pdb=" C HIS D 256 " pdb=" N GLU D 257 " pdb=" CA GLU D 257 " ideal model delta harmonic sigma weight residual -180.00 -135.49 -44.51 0 5.00e+00 4.00e-02 7.93e+01 ... (remaining 12853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2075 0.048 - 0.095: 908 0.095 - 0.143: 227 0.143 - 0.191: 81 0.191 - 0.238: 17 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB ILE D 199 " pdb=" CA ILE D 199 " pdb=" CG1 ILE D 199 " pdb=" CG2 ILE D 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE B 199 " pdb=" CA ILE B 199 " pdb=" CG1 ILE B 199 " pdb=" CG2 ILE B 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 199 " pdb=" CA ILE A 199 " pdb=" CG1 ILE A 199 " pdb=" CG2 ILE A 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3305 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 754 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO D 755 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A 755 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 754 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO B 755 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 755 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 755 " 0.042 5.00e-02 4.00e+02 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 636 2.70 - 3.25: 20772 3.25 - 3.80: 32076 3.80 - 4.35: 39228 4.35 - 4.90: 62291 Nonbonded interactions: 155003 Sorted by model distance: nonbonded pdb=" OE1 GLU A 751 " pdb=" OH TYR D 213 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR C 213 " pdb=" OE1 GLU D 751 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 460 " pdb=" OG SER D 607 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" OE1 GLU B 751 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 607 " pdb=" OH TYR B 460 " model vdw 2.282 3.040 ... (remaining 154998 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.660 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.040 Find NCS groups from input model: 0.190 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.006 0.060 21460 Z= 0.279 Angle : 1.184 14.755 29032 Z= 0.623 Chirality : 0.059 0.238 3308 Planarity : 0.007 0.078 3624 Dihedral : 12.600 74.915 7920 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.62 % Favored : 84.07 % Rotamer: Outliers : 0.87 % Allowed : 8.30 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.13 (0.11), residues: 2568 helix: -4.24 (0.07), residues: 1252 sheet: -4.71 (0.36), residues: 56 loop : -3.86 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 696 TYR 0.019 0.002 TYR C 382 PHE 0.019 0.003 PHE B 506 TRP 0.015 0.003 TRP B 742 HIS 0.019 0.003 HIS D 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.28 (21460) covalent geometry : angle 1.18368 / 0.62 (29032) hydrogen bonds : bond 0.31395 / 20.26 ( 736) hydrogen bonds : angle 9.86982 / 6.76 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 259 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8767 (mptt) REVERT: A 260 TYR cc_start: 0.8523 (t80) cc_final: 0.8278 (t80) REVERT: A 273 ASN cc_start: 0.8520 (t0) cc_final: 0.8257 (t0) REVERT: A 293 ASP cc_start: 0.7254 (m-30) cc_final: 0.6833 (m-30) REVERT: A 314 ASN cc_start: 0.7813 (t160) cc_final: 0.7378 (t0) REVERT: A 338 ASN cc_start: 0.7947 (p0) cc_final: 0.7641 (p0) REVERT: A 343 THR cc_start: 0.8519 (m) cc_final: 0.7638 (m) REVERT: A 355 GLU cc_start: 0.8408 (tp30) cc_final: 0.7823 (tp30) REVERT: A 376 LYS cc_start: 0.7481 (tptm) cc_final: 0.6947 (tptp) REVERT: A 409 TYR cc_start: 0.8689 (m-80) cc_final: 0.7223 (m-10) REVERT: A 440 MET cc_start: 0.7087 (mmt) cc_final: 0.6822 (mmt) REVERT: A 481 TRP cc_start: 0.5370 (t-100) cc_final: 0.4101 (t60) REVERT: A 539 LEU cc_start: 0.8645 (mt) cc_final: 0.8361 (mm) REVERT: A 542 PHE cc_start: 0.6827 (p90) cc_final: 0.6058 (p90) REVERT: A 555 MET cc_start: 0.9175 (mtt) cc_final: 0.8948 (mtp) REVERT: A 574 MET cc_start: 0.8472 (mtp) cc_final: 0.7980 (ttm) REVERT: A 582 VAL cc_start: 0.9143 (t) cc_final: 0.8908 (t) REVERT: A 633 PHE cc_start: 0.8200 (t80) cc_final: 0.7907 (t80) REVERT: A 670 LEU cc_start: 0.9359 (mm) cc_final: 0.8958 (mm) REVERT: A 706 MET cc_start: 0.7165 (ttt) cc_final: 0.6706 (tpp) outliers start: 5 outliers final: 1 residues processed: 263 average time/residue: 0.0702 time to fit residues: 23.8803 Evaluate side-chains 197 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.201 Evaluate side-chains 265 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 260 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8750 (mptt) REVERT: B 260 TYR cc_start: 0.8535 (t80) cc_final: 0.8291 (t80) REVERT: B 273 ASN cc_start: 0.8508 (t0) cc_final: 0.8261 (t0) REVERT: B 293 ASP cc_start: 0.7268 (m-30) cc_final: 0.6867 (m-30) REVERT: B 314 ASN cc_start: 0.7664 (t160) cc_final: 0.7253 (t0) REVERT: B 338 ASN cc_start: 0.8056 (p0) cc_final: 0.7721 (p0) REVERT: B 343 THR cc_start: 0.8549 (m) cc_final: 0.7673 (m) REVERT: B 355 GLU cc_start: 0.8398 (tp30) cc_final: 0.7795 (tp30) REVERT: B 376 LYS cc_start: 0.7455 (tptm) cc_final: 0.6918 (tptp) REVERT: B 382 TYR cc_start: 0.4824 (t80) cc_final: 0.4607 (t80) REVERT: B 409 TYR cc_start: 0.8705 (m-80) cc_final: 0.7099 (m-10) REVERT: B 439 TYR cc_start: 0.8279 (m-80) cc_final: 0.8078 (m-10) REVERT: B 440 MET cc_start: 0.7091 (mmt) cc_final: 0.6814 (mmt) REVERT: B 452 ASN cc_start: 0.9022 (m110) cc_final: 0.8793 (m110) REVERT: B 481 TRP cc_start: 0.5313 (t-100) cc_final: 0.4024 (t60) REVERT: B 539 LEU cc_start: 0.8692 (mt) cc_final: 0.7878 (mt) REVERT: B 555 MET cc_start: 0.9169 (mtt) cc_final: 0.8954 (mtp) REVERT: B 574 MET cc_start: 0.8493 (mtp) cc_final: 0.7941 (ttm) REVERT: B 582 VAL cc_start: 0.9150 (t) cc_final: 0.8933 (t) REVERT: B 633 PHE cc_start: 0.8091 (t80) cc_final: 0.7819 (t80) REVERT: B 670 LEU cc_start: 0.9374 (mm) cc_final: 0.8940 (mm) REVERT: B 758 ARG cc_start: 0.7625 (tpp80) cc_final: 0.6742 (ttt-90) outliers start: 5 outliers final: 1 residues processed: 264 average time/residue: 0.0719 time to fit residues: 24.6753 Evaluate side-chains 198 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 overall best weight: 3.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 452 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111635 restraints weight = 12632.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114826 restraints weight = 7309.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117040 restraints weight = 4913.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118629 restraints weight = 3669.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119777 restraints weight = 2934.904| |-----------------------------------------------------------------------------| r_work (final): 0.3513 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111681 restraints weight = 12680.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114818 restraints weight = 7510.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117107 restraints weight = 5133.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118706 restraints weight = 3834.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119761 restraints weight = 3082.592| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21460 Z= 0.157 Angle : 0.812 10.664 29032 Z= 0.410 Chirality : 0.044 0.184 3308 Planarity : 0.006 0.069 3624 Dihedral : 7.186 34.272 2808 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.32 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.14), residues: 2568 helix: -2.18 (0.12), residues: 1264 sheet: -3.91 (0.36), residues: 76 loop : -3.66 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.013 0.002 TYR B 260 PHE 0.017 0.002 PHE C 633 TRP 0.021 0.002 TRP C 742 HIS 0.010 0.002 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (21460) covalent geometry : angle 0.81209 / 0.41 (29032) hydrogen bonds : bond 0.05053 / 3.23 ( 736) hydrogen bonds : angle 5.51591 / 3.75 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8695 (mptt) REVERT: C 134 GLU cc_start: 0.8580 (mp0) cc_final: 0.8229 (tp30) REVERT: C 173 MET cc_start: 0.8590 (mtp) cc_final: 0.8250 (mtp) REVERT: C 293 ASP cc_start: 0.6934 (m-30) cc_final: 0.6637 (m-30) REVERT: C 338 ASN cc_start: 0.8538 (p0) cc_final: 0.8121 (p0) REVERT: C 342 LEU cc_start: 0.8147 (pt) cc_final: 0.7741 (pp) REVERT: C 355 GLU cc_start: 0.8449 (tp30) cc_final: 0.7708 (tp30) REVERT: C 359 TYR cc_start: 0.8429 (t80) cc_final: 0.8115 (t80) REVERT: C 542 PHE cc_start: 0.6835 (p90) cc_final: 0.6161 (p90) REVERT: C 555 MET cc_start: 0.9394 (mtt) cc_final: 0.8995 (mtt) REVERT: C 574 MET cc_start: 0.8517 (mtp) cc_final: 0.7924 (ttm) REVERT: C 578 MET cc_start: 0.8533 (tpp) cc_final: 0.8329 (mmt) REVERT: C 650 TYR cc_start: 0.4813 (m-10) cc_final: 0.4511 (t80) REVERT: C 663 ILE cc_start: 0.9159 (tp) cc_final: 0.8954 (tp) REVERT: C 673 LEU cc_start: 0.9009 (tp) cc_final: 0.8594 (tp) REVERT: C 699 THR cc_start: 0.9186 (t) cc_final: 0.8909 (m) REVERT: C 702 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 705 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8350 (mttt) REVERT: C 706 MET cc_start: 0.7585 (ttt) cc_final: 0.7029 (tpp) REVERT: C 758 ARG cc_start: 0.7561 (tpp80) cc_final: 0.6638 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0648 time to fit residues: 18.1963 Evaluate side-chains 175 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.202 Evaluate side-chains 203 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.207 Fit side-chains REVERT: D 121 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8691 (mptt) REVERT: D 134 GLU cc_start: 0.8482 (mp0) cc_final: 0.8123 (tp30) REVERT: D 173 MET cc_start: 0.8599 (mtp) cc_final: 0.8244 (mtp) REVERT: D 293 ASP cc_start: 0.6905 (m-30) cc_final: 0.6616 (m-30) REVERT: D 338 ASN cc_start: 0.8474 (p0) cc_final: 0.8104 (p0) REVERT: D 342 LEU cc_start: 0.8063 (pt) cc_final: 0.7303 (pp) REVERT: D 355 GLU cc_start: 0.8438 (tp30) cc_final: 0.7722 (tp30) REVERT: D 359 TYR cc_start: 0.8430 (t80) cc_final: 0.8136 (t80) REVERT: D 555 MET cc_start: 0.9384 (mtt) cc_final: 0.8954 (mtt) REVERT: D 574 MET cc_start: 0.8506 (mtp) cc_final: 0.7803 (ttm) REVERT: D 650 TYR cc_start: 0.4830 (m-10) cc_final: 0.4511 (t80) REVERT: D 673 LEU cc_start: 0.9027 (tp) cc_final: 0.8616 (tp) REVERT: D 677 MET cc_start: 0.8396 (mmp) cc_final: 0.8050 (mtp) REVERT: D 699 THR cc_start: 0.9219 (t) cc_final: 0.8922 (m) REVERT: D 702 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7812 (mm-30) REVERT: D 705 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8400 (mttt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0619 time to fit residues: 16.9072 Evaluate side-chains 172 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 211 optimal weight: 0.0370 chunk 136 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 212 optimal weight: 4.9990 chunk 44 optimal weight: 0.0050 chunk 179 optimal weight: 20.0000 chunk 4 optimal weight: 0.2980 overall best weight: 1.6676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 GLN C 452 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 314 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 452 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114117 restraints weight = 12606.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117303 restraints weight = 7493.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119586 restraints weight = 5103.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121187 restraints weight = 3812.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122304 restraints weight = 3057.302| |-----------------------------------------------------------------------------| r_work (final): 0.3551 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113010 restraints weight = 12741.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116270 restraints weight = 7512.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118536 restraints weight = 5107.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120068 restraints weight = 3832.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121288 restraints weight = 3087.392| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21460 Z= 0.127 Angle : 0.753 10.126 29032 Z= 0.378 Chirality : 0.043 0.197 3308 Planarity : 0.005 0.066 3624 Dihedral : 6.755 36.408 2808 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.63 % Favored : 86.21 % Rotamer: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.15), residues: 2568 helix: -1.33 (0.13), residues: 1300 sheet: -4.15 (0.33), residues: 76 loop : -3.61 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.023 0.001 TYR D 575 PHE 0.024 0.002 PHE A 633 TRP 0.016 0.001 TRP A 742 HIS 0.008 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (21460) covalent geometry : angle 0.75303 / 0.38 (29032) hydrogen bonds : bond 0.03930 / 2.53 ( 736) hydrogen bonds : angle 4.86491 / 3.26 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.247 Fit side-chains REVERT: C 121 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8706 (mptt) REVERT: C 260 TYR cc_start: 0.8956 (t80) cc_final: 0.8639 (t80) REVERT: C 293 ASP cc_start: 0.6791 (m-30) cc_final: 0.6320 (m-30) REVERT: C 338 ASN cc_start: 0.8394 (p0) cc_final: 0.7720 (p0) REVERT: C 342 LEU cc_start: 0.7978 (pt) cc_final: 0.7564 (pp) REVERT: C 355 GLU cc_start: 0.8458 (tp30) cc_final: 0.7836 (tp30) REVERT: C 391 ASP cc_start: 0.7516 (t70) cc_final: 0.7136 (t70) REVERT: C 409 TYR cc_start: 0.8183 (m-80) cc_final: 0.7506 (m-80) REVERT: C 440 MET cc_start: 0.7238 (mmt) cc_final: 0.7001 (tpp) REVERT: C 542 PHE cc_start: 0.6882 (p90) cc_final: 0.6277 (p90) REVERT: C 555 MET cc_start: 0.9389 (mtt) cc_final: 0.9030 (mtt) REVERT: C 574 MET cc_start: 0.8458 (mtp) cc_final: 0.7994 (ttm) REVERT: C 576 SER cc_start: 0.9203 (t) cc_final: 0.8690 (p) REVERT: C 578 MET cc_start: 0.8571 (tpp) cc_final: 0.8262 (mmt) REVERT: C 589 LYS cc_start: 0.8177 (mttt) cc_final: 0.7316 (tptt) REVERT: C 625 PHE cc_start: 0.6871 (t80) cc_final: 0.6619 (t80) REVERT: C 650 TYR cc_start: 0.4591 (m-10) cc_final: 0.4358 (t80) REVERT: C 702 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8097 (mm-30) REVERT: C 706 MET cc_start: 0.7574 (ttt) cc_final: 0.6956 (tpp) REVERT: C 758 ARG cc_start: 0.7605 (tpp80) cc_final: 0.6652 (ttt-90) outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.0637 time to fit residues: 16.7466 Evaluate side-chains 167 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.204 Evaluate side-chains 196 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8706 (mptt) REVERT: D 260 TYR cc_start: 0.8932 (t80) cc_final: 0.8621 (t80) REVERT: D 293 ASP cc_start: 0.6775 (m-30) cc_final: 0.6309 (m-30) REVERT: D 315 ASP cc_start: 0.6928 (t70) cc_final: 0.6593 (t70) REVERT: D 319 ARG cc_start: 0.9008 (mtt180) cc_final: 0.8761 (ttm110) REVERT: D 338 ASN cc_start: 0.8204 (p0) cc_final: 0.7764 (p0) REVERT: D 346 GLN cc_start: 0.8772 (pt0) cc_final: 0.8332 (pt0) REVERT: D 355 GLU cc_start: 0.8325 (tp30) cc_final: 0.7704 (tp30) REVERT: D 382 TYR cc_start: 0.5224 (t80) cc_final: 0.4736 (t80) REVERT: D 391 ASP cc_start: 0.7631 (t70) cc_final: 0.7251 (t70) REVERT: D 409 TYR cc_start: 0.8042 (m-80) cc_final: 0.7337 (m-80) REVERT: D 501 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7444 (mm-30) REVERT: D 555 MET cc_start: 0.9381 (mtt) cc_final: 0.9031 (mtt) REVERT: D 574 MET cc_start: 0.8495 (mtp) cc_final: 0.8029 (ttm) REVERT: D 576 SER cc_start: 0.9155 (t) cc_final: 0.8664 (p) REVERT: D 589 LYS cc_start: 0.8166 (mttt) cc_final: 0.7389 (tptt) REVERT: D 650 TYR cc_start: 0.4717 (m-10) cc_final: 0.4467 (t80) REVERT: D 699 THR cc_start: 0.9297 (t) cc_final: 0.9093 (p) REVERT: D 702 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8020 (mm-30) REVERT: D 706 MET cc_start: 0.8286 (tpt) cc_final: 0.7301 (tpp) REVERT: D 758 ARG cc_start: 0.7592 (tpp80) cc_final: 0.6798 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0679 time to fit residues: 17.6905 Evaluate side-chains 166 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 145 optimal weight: 5.9990 chunk 163 optimal weight: 0.1980 chunk 226 optimal weight: 10.0000 chunk 138 optimal weight: 0.0470 chunk 229 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 212 optimal weight: 0.4980 chunk 149 optimal weight: 0.0270 chunk 40 optimal weight: 0.0470 chunk 139 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 417 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 417 HIS ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116929 restraints weight = 13091.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120356 restraints weight = 7934.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122758 restraints weight = 5451.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124420 restraints weight = 4091.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125651 restraints weight = 3296.348| |-----------------------------------------------------------------------------| r_work (final): 0.3604 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116201 restraints weight = 12777.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119552 restraints weight = 7769.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122004 restraints weight = 5328.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123616 restraints weight = 3980.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124908 restraints weight = 3194.690| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21460 Z= 0.125 Angle : 0.722 10.075 29032 Z= 0.360 Chirality : 0.042 0.163 3308 Planarity : 0.005 0.062 3624 Dihedral : 6.373 35.413 2808 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.77 % Favored : 87.07 % Rotamer: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.15), residues: 2568 helix: -0.96 (0.14), residues: 1316 sheet: -4.10 (0.35), residues: 76 loop : -3.67 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.010 0.001 TYR B 321 PHE 0.020 0.001 PHE B 625 TRP 0.027 0.001 TRP D 742 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (21460) covalent geometry : angle 0.72220 / 0.36 (29032) hydrogen bonds : bond 0.03448 / 2.23 ( 736) hydrogen bonds : angle 4.44554 / 2.97 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.214 Fit side-chains REVERT: C 121 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8731 (mptt) REVERT: C 135 LEU cc_start: 0.8734 (tp) cc_final: 0.8533 (tp) REVERT: C 195 GLU cc_start: 0.7886 (tp30) cc_final: 0.6946 (tm-30) REVERT: C 213 TYR cc_start: 0.7326 (p90) cc_final: 0.6959 (p90) REVERT: C 281 LEU cc_start: 0.9118 (mt) cc_final: 0.8860 (mp) REVERT: C 338 ASN cc_start: 0.8327 (p0) cc_final: 0.7524 (p0) REVERT: C 342 LEU cc_start: 0.7602 (pt) cc_final: 0.7240 (pp) REVERT: C 355 GLU cc_start: 0.8435 (tp30) cc_final: 0.7697 (tp30) REVERT: C 356 ILE cc_start: 0.9564 (tt) cc_final: 0.9307 (mm) REVERT: C 359 TYR cc_start: 0.8283 (t80) cc_final: 0.7739 (t80) REVERT: C 417 HIS cc_start: 0.8122 (p90) cc_final: 0.7907 (p90) REVERT: C 433 TRP cc_start: 0.8863 (t60) cc_final: 0.8580 (t60) REVERT: C 481 TRP cc_start: 0.5899 (m100) cc_final: 0.4949 (t-100) REVERT: C 501 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 542 PHE cc_start: 0.7000 (p90) cc_final: 0.6471 (p90) REVERT: C 555 MET cc_start: 0.9419 (mtt) cc_final: 0.9185 (mtt) REVERT: C 567 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8169 (ptp-170) REVERT: C 574 MET cc_start: 0.8374 (mtp) cc_final: 0.7846 (ttm) REVERT: C 589 LYS cc_start: 0.8036 (mttt) cc_final: 0.7456 (tmtt) REVERT: C 625 PHE cc_start: 0.6529 (t80) cc_final: 0.5990 (t80) REVERT: C 702 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8264 (mm-30) REVERT: C 706 MET cc_start: 0.7531 (ttt) cc_final: 0.6673 (tpp) REVERT: C 722 LYS cc_start: 0.7477 (mtmt) cc_final: 0.6740 (mttt) REVERT: C 758 ARG cc_start: 0.7732 (tpp80) cc_final: 0.6941 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.0620 time to fit residues: 16.5755 Evaluate side-chains 167 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.202 Evaluate side-chains 191 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8722 (mptt) REVERT: D 261 PHE cc_start: 0.8468 (p90) cc_final: 0.8123 (p90) REVERT: D 338 ASN cc_start: 0.8094 (p0) cc_final: 0.7545 (p0) REVERT: D 346 GLN cc_start: 0.8863 (pt0) cc_final: 0.8499 (pt0) REVERT: D 355 GLU cc_start: 0.8448 (tp30) cc_final: 0.7666 (tm-30) REVERT: D 356 ILE cc_start: 0.9536 (tt) cc_final: 0.8874 (mm) REVERT: D 359 TYR cc_start: 0.8278 (t80) cc_final: 0.7731 (t80) REVERT: D 391 ASP cc_start: 0.7588 (t70) cc_final: 0.7186 (t70) REVERT: D 501 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7368 (mm-30) REVERT: D 555 MET cc_start: 0.9407 (mtt) cc_final: 0.9120 (mtt) REVERT: D 567 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8637 (mtt180) REVERT: D 574 MET cc_start: 0.8429 (mtp) cc_final: 0.7976 (ttm) REVERT: D 589 LYS cc_start: 0.8055 (mttt) cc_final: 0.7463 (tmtt) REVERT: D 625 PHE cc_start: 0.6592 (t80) cc_final: 0.6148 (t80) REVERT: D 706 MET cc_start: 0.8298 (tpt) cc_final: 0.7017 (tpp) REVERT: D 758 ARG cc_start: 0.7767 (tpp80) cc_final: 0.7034 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0660 time to fit residues: 16.8219 Evaluate side-chains 166 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 9.9990 chunk 210 optimal weight: 0.0270 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 123 optimal weight: 0.0040 chunk 211 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 292 GLN C 313 GLN C 426 HIS C 471 HIS C 647 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN D 242 ASN D 301 HIS D 313 GLN D 346 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121870 restraints weight = 13373.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124953 restraints weight = 8327.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127164 restraints weight = 5882.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128621 restraints weight = 4508.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129825 restraints weight = 3711.703| |-----------------------------------------------------------------------------| r_work (final): 0.3645 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119159 restraints weight = 13248.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122310 restraints weight = 8282.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124599 restraints weight = 5831.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126154 restraints weight = 4442.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127288 restraints weight = 3624.634| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21460 Z= 0.122 Angle : 0.709 9.921 29032 Z= 0.354 Chirality : 0.041 0.140 3308 Planarity : 0.005 0.057 3624 Dihedral : 6.239 39.497 2808 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.71 % Favored : 86.29 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.16), residues: 2568 helix: -0.65 (0.14), residues: 1328 sheet: -4.08 (0.34), residues: 76 loop : -3.55 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 693 TYR 0.012 0.001 TYR C 382 PHE 0.024 0.001 PHE C 447 TRP 0.024 0.001 TRP A 742 HIS 0.010 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21460) covalent geometry : angle 0.70938 / 0.35 (29032) hydrogen bonds : bond 0.03149 / 2.05 ( 736) hydrogen bonds : angle 4.42136 / 2.95 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8713 (mptt) REVERT: C 135 LEU cc_start: 0.8788 (tp) cc_final: 0.8561 (tp) REVERT: C 159 MET cc_start: 0.7549 (mtp) cc_final: 0.7340 (mtp) REVERT: C 195 GLU cc_start: 0.7663 (tp30) cc_final: 0.6946 (tm-30) REVERT: C 338 ASN cc_start: 0.8174 (p0) cc_final: 0.7353 (p0) REVERT: C 342 LEU cc_start: 0.7441 (pt) cc_final: 0.7152 (pp) REVERT: C 355 GLU cc_start: 0.8391 (tp30) cc_final: 0.7847 (tp30) REVERT: C 356 ILE cc_start: 0.9558 (tt) cc_final: 0.9284 (mm) REVERT: C 387 SER cc_start: 0.8592 (t) cc_final: 0.7983 (p) REVERT: C 409 TYR cc_start: 0.7774 (m-80) cc_final: 0.6440 (m-10) REVERT: C 433 TRP cc_start: 0.8796 (t60) cc_final: 0.8543 (t60) REVERT: C 481 TRP cc_start: 0.5846 (m100) cc_final: 0.4959 (t-100) REVERT: C 485 LEU cc_start: 0.7954 (mp) cc_final: 0.7598 (mt) REVERT: C 501 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 542 PHE cc_start: 0.6990 (p90) cc_final: 0.6450 (p90) REVERT: C 555 MET cc_start: 0.9473 (mtt) cc_final: 0.9238 (mtt) REVERT: C 574 MET cc_start: 0.8325 (mtp) cc_final: 0.7866 (ttm) REVERT: C 589 LYS cc_start: 0.8041 (mttt) cc_final: 0.7585 (tmtt) REVERT: C 695 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8664 (mm-40) REVERT: C 699 THR cc_start: 0.9018 (t) cc_final: 0.8742 (m) REVERT: C 702 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 706 MET cc_start: 0.7583 (ttt) cc_final: 0.6827 (tpp) REVERT: C 722 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6931 (mtmt) REVERT: C 758 ARG cc_start: 0.7688 (tpp80) cc_final: 0.6998 (ttt180) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0611 time to fit residues: 15.7413 Evaluate side-chains 164 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.207 Evaluate side-chains 195 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.159 Fit side-chains REVERT: B 121 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8801 (mptt) REVERT: B 159 MET cc_start: 0.7473 (mtp) cc_final: 0.7258 (mtp) REVERT: B 195 GLU cc_start: 0.7855 (tp30) cc_final: 0.6814 (tm-30) REVERT: B 261 PHE cc_start: 0.8174 (p90) cc_final: 0.7803 (p90) REVERT: B 281 LEU cc_start: 0.8974 (mp) cc_final: 0.8759 (mp) REVERT: B 282 MET cc_start: 0.7999 (tmm) cc_final: 0.7759 (tpp) REVERT: B 338 ASN cc_start: 0.8209 (p0) cc_final: 0.7599 (p0) REVERT: B 355 GLU cc_start: 0.8403 (tp30) cc_final: 0.7759 (tp30) REVERT: B 356 ILE cc_start: 0.9518 (tt) cc_final: 0.9259 (mm) REVERT: B 359 TYR cc_start: 0.8275 (t80) cc_final: 0.8044 (t80) REVERT: B 387 SER cc_start: 0.8568 (t) cc_final: 0.8116 (p) REVERT: B 391 ASP cc_start: 0.7604 (t70) cc_final: 0.7390 (t70) REVERT: B 409 TYR cc_start: 0.8118 (m-80) cc_final: 0.6679 (m-10) REVERT: B 481 TRP cc_start: 0.5903 (m100) cc_final: 0.4905 (t-100) REVERT: B 501 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 555 MET cc_start: 0.9420 (mtt) cc_final: 0.9204 (mtt) REVERT: B 562 MET cc_start: 0.8858 (ppp) cc_final: 0.8015 (ppp) REVERT: B 574 MET cc_start: 0.8349 (mtp) cc_final: 0.7896 (ttm) REVERT: B 589 LYS cc_start: 0.7930 (mttt) cc_final: 0.7451 (tmtt) REVERT: B 625 PHE cc_start: 0.6294 (t80) cc_final: 0.5887 (t80) REVERT: B 702 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 758 ARG cc_start: 0.7889 (tpp80) cc_final: 0.7043 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0629 time to fit residues: 16.3589 Evaluate side-chains 167 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 149 optimal weight: 0.0170 chunk 172 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS B 346 GLN B 647 ASN B 695 GLN C 279 GLN C 292 GLN C 301 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115934 restraints weight = 13623.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118934 restraints weight = 8533.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121072 restraints weight = 6037.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122622 restraints weight = 4657.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123641 restraints weight = 3821.979| |-----------------------------------------------------------------------------| r_work (final): 0.3575 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115478 restraints weight = 13579.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118456 restraints weight = 8634.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120635 restraints weight = 6104.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122083 restraints weight = 4715.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123236 restraints weight = 3890.763| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21460 Z= 0.136 Angle : 0.731 9.745 29032 Z= 0.365 Chirality : 0.042 0.145 3308 Planarity : 0.005 0.057 3624 Dihedral : 6.207 39.494 2808 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.16), residues: 2568 helix: -0.34 (0.14), residues: 1348 sheet: -3.77 (0.43), residues: 76 loop : -3.40 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 693 TYR 0.025 0.001 TYR C 650 PHE 0.014 0.001 PHE D 625 TRP 0.018 0.001 TRP D 742 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (21460) covalent geometry : angle 0.73078 / 0.36 (29032) hydrogen bonds : bond 0.03227 / 2.04 ( 736) hydrogen bonds : angle 4.29704 / 2.89 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8755 (mptt) REVERT: C 159 MET cc_start: 0.7507 (mtp) cc_final: 0.7224 (mtp) REVERT: C 338 ASN cc_start: 0.8371 (p0) cc_final: 0.7599 (p0) REVERT: C 342 LEU cc_start: 0.7409 (pt) cc_final: 0.7154 (pp) REVERT: C 355 GLU cc_start: 0.8355 (tp30) cc_final: 0.7923 (tp30) REVERT: C 356 ILE cc_start: 0.9599 (tt) cc_final: 0.9317 (mm) REVERT: C 387 SER cc_start: 0.8521 (t) cc_final: 0.7966 (p) REVERT: C 481 TRP cc_start: 0.5875 (m100) cc_final: 0.5000 (t-100) REVERT: C 485 LEU cc_start: 0.7985 (mp) cc_final: 0.7693 (mt) REVERT: C 501 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7336 (mm-30) REVERT: C 522 PHE cc_start: 0.7121 (m-10) cc_final: 0.6861 (m-10) REVERT: C 542 PHE cc_start: 0.6969 (p90) cc_final: 0.6600 (p90) REVERT: C 555 MET cc_start: 0.9432 (mtt) cc_final: 0.9193 (mtt) REVERT: C 567 ARG cc_start: 0.8713 (mtt180) cc_final: 0.7958 (ptp-110) REVERT: C 574 MET cc_start: 0.8333 (mtp) cc_final: 0.7812 (ttm) REVERT: C 589 LYS cc_start: 0.8092 (mttt) cc_final: 0.7590 (tmtt) REVERT: C 634 LYS cc_start: 0.8271 (tttt) cc_final: 0.7777 (tttt) REVERT: C 699 THR cc_start: 0.9027 (t) cc_final: 0.8338 (p) REVERT: C 702 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7683 (mp0) REVERT: C 706 MET cc_start: 0.7752 (ttt) cc_final: 0.6982 (tpp) REVERT: C 730 LEU cc_start: 0.8449 (mp) cc_final: 0.8242 (mp) REVERT: C 743 LYS cc_start: 0.7916 (pttm) cc_final: 0.7547 (pttm) REVERT: C 758 ARG cc_start: 0.7925 (tpp80) cc_final: 0.6984 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.0606 time to fit residues: 15.4811 Evaluate side-chains 163 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.199 Evaluate side-chains 188 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.204 Fit side-chains REVERT: D 121 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8707 (mptt) REVERT: D 159 MET cc_start: 0.7504 (mtp) cc_final: 0.7209 (mtp) REVERT: D 173 MET cc_start: 0.8483 (mtp) cc_final: 0.8190 (mtp) REVERT: D 195 GLU cc_start: 0.7679 (tp30) cc_final: 0.6753 (tm-30) REVERT: D 284 ASN cc_start: 0.9160 (t0) cc_final: 0.8801 (t0) REVERT: D 338 ASN cc_start: 0.8432 (p0) cc_final: 0.8165 (p0) REVERT: D 355 GLU cc_start: 0.8379 (tp30) cc_final: 0.7967 (tp30) REVERT: D 356 ILE cc_start: 0.9563 (tt) cc_final: 0.9292 (mm) REVERT: D 359 TYR cc_start: 0.8386 (t80) cc_final: 0.8077 (t80) REVERT: D 387 SER cc_start: 0.8495 (t) cc_final: 0.7957 (p) REVERT: D 391 ASP cc_start: 0.7647 (t70) cc_final: 0.7361 (t70) REVERT: D 409 TYR cc_start: 0.8114 (m-80) cc_final: 0.6337 (m-10) REVERT: D 439 TYR cc_start: 0.7371 (m-10) cc_final: 0.7079 (m-10) REVERT: D 481 TRP cc_start: 0.5852 (m100) cc_final: 0.4947 (t-100) REVERT: D 501 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7345 (mm-30) REVERT: D 555 MET cc_start: 0.9459 (mtt) cc_final: 0.9184 (mtt) REVERT: D 562 MET cc_start: 0.8889 (ppp) cc_final: 0.7990 (ppp) REVERT: D 579 ILE cc_start: 0.8852 (tp) cc_final: 0.8459 (mm) REVERT: D 589 LYS cc_start: 0.7916 (mttt) cc_final: 0.7523 (tmtt) REVERT: D 625 PHE cc_start: 0.6332 (t80) cc_final: 0.5832 (t80) REVERT: D 695 GLN cc_start: 0.9009 (tp40) cc_final: 0.8705 (mm-40) REVERT: D 702 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 758 ARG cc_start: 0.7910 (tpp80) cc_final: 0.6958 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0601 time to fit residues: 15.3986 Evaluate side-chains 164 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 76 optimal weight: 30.0000 chunk 217 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 85 optimal weight: 0.0470 chunk 142 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 overall best weight: 4.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 GLN C 279 GLN C 301 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 346 GLN D 647 ASN D 695 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116356 restraints weight = 13708.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119273 restraints weight = 8736.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121326 restraints weight = 6246.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122821 restraints weight = 4846.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123910 restraints weight = 3995.320| |-----------------------------------------------------------------------------| r_work (final): 0.3549 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113533 restraints weight = 13606.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116472 restraints weight = 8562.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118482 restraints weight = 6071.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120052 restraints weight = 4697.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121076 restraints weight = 3855.629| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21460 Z= 0.138 Angle : 0.733 9.652 29032 Z= 0.366 Chirality : 0.043 0.157 3308 Planarity : 0.005 0.059 3624 Dihedral : 6.193 39.873 2808 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.16), residues: 2568 helix: -0.19 (0.14), residues: 1332 sheet: -3.49 (0.53), residues: 68 loop : -3.34 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 226 TYR 0.032 0.002 TYR B 460 PHE 0.038 0.002 PHE A 625 TRP 0.018 0.001 TRP D 742 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (21460) covalent geometry : angle 0.73269 / 0.37 (29032) hydrogen bonds : bond 0.03109 / 1.98 ( 736) hydrogen bonds : angle 4.35941 / 2.94 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8767 (mptt) REVERT: C 159 MET cc_start: 0.7420 (mtp) cc_final: 0.7126 (mtp) REVERT: C 195 GLU cc_start: 0.7604 (tp30) cc_final: 0.6591 (tm-30) REVERT: C 283 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7955 (mp0) REVERT: C 338 ASN cc_start: 0.8342 (p0) cc_final: 0.7624 (p0) REVERT: C 355 GLU cc_start: 0.8390 (tp30) cc_final: 0.7870 (tp30) REVERT: C 356 ILE cc_start: 0.9579 (tt) cc_final: 0.9251 (mm) REVERT: C 387 SER cc_start: 0.8507 (t) cc_final: 0.8005 (p) REVERT: C 391 ASP cc_start: 0.7382 (t70) cc_final: 0.6793 (t70) REVERT: C 481 TRP cc_start: 0.5605 (m100) cc_final: 0.4814 (t-100) REVERT: C 485 LEU cc_start: 0.8039 (mp) cc_final: 0.7781 (mt) REVERT: C 542 PHE cc_start: 0.6978 (p90) cc_final: 0.6401 (p90) REVERT: C 555 MET cc_start: 0.9459 (mtt) cc_final: 0.9192 (mtt) REVERT: C 567 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8289 (mtp85) REVERT: C 583 ILE cc_start: 0.7695 (pt) cc_final: 0.7479 (tp) REVERT: C 589 LYS cc_start: 0.8027 (mttt) cc_final: 0.7571 (tmtt) REVERT: C 634 LYS cc_start: 0.8351 (tttt) cc_final: 0.8032 (tttt) REVERT: C 699 THR cc_start: 0.9063 (t) cc_final: 0.8366 (p) REVERT: C 702 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7607 (mp0) REVERT: C 706 MET cc_start: 0.7803 (ttt) cc_final: 0.6973 (tpp) REVERT: C 758 ARG cc_start: 0.7931 (tpp80) cc_final: 0.6912 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0608 time to fit residues: 15.1913 Evaluate side-chains 158 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.208 Evaluate side-chains 182 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.212 Fit side-chains REVERT: D 121 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8764 (mptt) REVERT: D 135 LEU cc_start: 0.8884 (tp) cc_final: 0.8645 (tp) REVERT: D 159 MET cc_start: 0.7427 (mtp) cc_final: 0.7145 (mtp) REVERT: D 195 GLU cc_start: 0.7680 (tp30) cc_final: 0.6862 (tm-30) REVERT: D 260 TYR cc_start: 0.8715 (t80) cc_final: 0.8379 (t80) REVERT: D 261 PHE cc_start: 0.8436 (p90) cc_final: 0.8155 (p90) REVERT: D 277 ILE cc_start: 0.9169 (tt) cc_final: 0.8952 (tt) REVERT: D 284 ASN cc_start: 0.9070 (t0) cc_final: 0.8755 (t0) REVERT: D 293 ASP cc_start: 0.6880 (m-30) cc_final: 0.5235 (m-30) REVERT: D 338 ASN cc_start: 0.8600 (p0) cc_final: 0.8243 (p0) REVERT: D 355 GLU cc_start: 0.8487 (tp30) cc_final: 0.7982 (tp30) REVERT: D 356 ILE cc_start: 0.9570 (tt) cc_final: 0.9294 (mm) REVERT: D 387 SER cc_start: 0.8494 (t) cc_final: 0.7991 (p) REVERT: D 391 ASP cc_start: 0.7689 (t70) cc_final: 0.7439 (t70) REVERT: D 409 TYR cc_start: 0.8036 (m-80) cc_final: 0.6331 (m-10) REVERT: D 481 TRP cc_start: 0.5874 (m100) cc_final: 0.4929 (t-100) REVERT: D 555 MET cc_start: 0.9434 (mtt) cc_final: 0.9055 (mtt) REVERT: D 562 MET cc_start: 0.8897 (ppp) cc_final: 0.7984 (ppp) REVERT: D 574 MET cc_start: 0.8271 (mtp) cc_final: 0.7531 (tpp) REVERT: D 589 LYS cc_start: 0.8112 (mttt) cc_final: 0.7672 (tmtt) REVERT: D 625 PHE cc_start: 0.6269 (t80) cc_final: 0.5938 (t80) REVERT: D 695 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8478 (mm-40) REVERT: D 702 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7645 (mm-30) REVERT: D 758 ARG cc_start: 0.7913 (tpp80) cc_final: 0.6827 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0589 time to fit residues: 14.6741 Evaluate side-chains 160 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 69 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 232 optimal weight: 0.0370 chunk 247 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 156 optimal weight: 0.1980 chunk 169 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 GLN C 301 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 346 GLN D 647 ASN D 695 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118976 restraints weight = 13364.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121974 restraints weight = 8405.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124127 restraints weight = 5970.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125554 restraints weight = 4609.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126727 restraints weight = 3813.399| |-----------------------------------------------------------------------------| r_work (final): 0.3614 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118258 restraints weight = 13472.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121195 restraints weight = 8591.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123333 restraints weight = 6119.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124865 restraints weight = 4748.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125885 restraints weight = 3906.696| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21460 Z= 0.124 Angle : 0.737 10.363 29032 Z= 0.362 Chirality : 0.042 0.195 3308 Planarity : 0.004 0.056 3624 Dihedral : 6.052 39.964 2808 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.17), residues: 2568 helix: -0.29 (0.14), residues: 1368 sheet: -3.57 (0.54), residues: 68 loop : -3.37 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 757 TYR 0.017 0.001 TYR C 650 PHE 0.018 0.001 PHE A 259 TRP 0.024 0.001 TRP D 742 HIS 0.009 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21460) covalent geometry : angle 0.73717 / 0.36 (29032) hydrogen bonds : bond 0.02999 / 1.93 ( 736) hydrogen bonds : angle 4.18284 / 2.81 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8736 (mptt) REVERT: C 160 HIS cc_start: 0.7551 (t-90) cc_final: 0.6969 (t70) REVERT: C 195 GLU cc_start: 0.7389 (tp30) cc_final: 0.6506 (tm-30) REVERT: C 261 PHE cc_start: 0.8252 (p90) cc_final: 0.7889 (p90) REVERT: C 279 GLN cc_start: 0.8630 (tp40) cc_final: 0.7882 (mm110) REVERT: C 282 MET cc_start: 0.8119 (tmm) cc_final: 0.6961 (tmm) REVERT: C 283 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7869 (mp0) REVERT: C 327 ARG cc_start: 0.7186 (tpp-160) cc_final: 0.6921 (tpp-160) REVERT: C 338 ASN cc_start: 0.7999 (p0) cc_final: 0.7445 (p0) REVERT: C 355 GLU cc_start: 0.8304 (tp30) cc_final: 0.8006 (tp30) REVERT: C 387 SER cc_start: 0.8175 (t) cc_final: 0.7554 (p) REVERT: C 433 TRP cc_start: 0.8908 (t60) cc_final: 0.8490 (t60) REVERT: C 481 TRP cc_start: 0.5851 (m100) cc_final: 0.5014 (t-100) REVERT: C 485 LEU cc_start: 0.7827 (mp) cc_final: 0.7622 (mt) REVERT: C 542 PHE cc_start: 0.7026 (p90) cc_final: 0.6528 (p90) REVERT: C 555 MET cc_start: 0.9434 (mtt) cc_final: 0.9143 (mtt) REVERT: C 562 MET cc_start: 0.8888 (ppp) cc_final: 0.8130 (ppp) REVERT: C 574 MET cc_start: 0.8245 (mtp) cc_final: 0.6828 (mmm) REVERT: C 589 LYS cc_start: 0.7929 (mttt) cc_final: 0.7516 (tmtt) REVERT: C 634 LYS cc_start: 0.8342 (tttt) cc_final: 0.8099 (tttt) REVERT: C 689 GLU cc_start: 0.8242 (tp30) cc_final: 0.7750 (mm-30) REVERT: C 699 THR cc_start: 0.9007 (t) cc_final: 0.8232 (p) REVERT: C 702 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7582 (mt-10) REVERT: C 706 MET cc_start: 0.7655 (ttt) cc_final: 0.6933 (tpp) REVERT: C 758 ARG cc_start: 0.7935 (tpp80) cc_final: 0.6880 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0610 time to fit residues: 15.3550 Evaluate side-chains 160 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.272 Evaluate side-chains 186 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.217 Fit side-chains REVERT: D 121 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8749 (mptt) REVERT: D 195 GLU cc_start: 0.7584 (tp30) cc_final: 0.6778 (tm-30) REVERT: D 277 ILE cc_start: 0.9165 (tt) cc_final: 0.8958 (tt) REVERT: D 283 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7791 (mp0) REVERT: D 284 ASN cc_start: 0.9068 (t0) cc_final: 0.8806 (t0) REVERT: D 338 ASN cc_start: 0.8352 (p0) cc_final: 0.7959 (p0) REVERT: D 355 GLU cc_start: 0.8422 (tp30) cc_final: 0.7943 (tp30) REVERT: D 356 ILE cc_start: 0.9492 (tt) cc_final: 0.9130 (mm) REVERT: D 387 SER cc_start: 0.8147 (t) cc_final: 0.7600 (p) REVERT: D 391 ASP cc_start: 0.7359 (t70) cc_final: 0.6740 (t70) REVERT: D 409 TYR cc_start: 0.8003 (m-80) cc_final: 0.6134 (m-10) REVERT: D 433 TRP cc_start: 0.9033 (t60) cc_final: 0.8633 (t60) REVERT: D 481 TRP cc_start: 0.5819 (m100) cc_final: 0.4873 (t-100) REVERT: D 555 MET cc_start: 0.9403 (mtt) cc_final: 0.9076 (mtt) REVERT: D 562 MET cc_start: 0.8818 (ppp) cc_final: 0.8007 (ppp) REVERT: D 567 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7988 (mtp180) REVERT: D 574 MET cc_start: 0.8257 (mtp) cc_final: 0.7462 (mmm) REVERT: D 589 LYS cc_start: 0.8109 (mttt) cc_final: 0.7739 (tmtt) REVERT: D 702 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7558 (mm-30) REVERT: D 732 LEU cc_start: 0.7988 (mt) cc_final: 0.7726 (mt) REVERT: D 758 ARG cc_start: 0.8058 (tpp80) cc_final: 0.6929 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0643 time to fit residues: 15.9682 Evaluate side-chains 155 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 107 optimal weight: 0.7980 chunk 221 optimal weight: 0.0980 chunk 179 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 301 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 346 GLN D 647 ASN D 695 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121240 restraints weight = 13608.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124276 restraints weight = 8581.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126437 restraints weight = 6106.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127996 restraints weight = 4714.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129085 restraints weight = 3883.260| |-----------------------------------------------------------------------------| r_work (final): 0.3630 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118443 restraints weight = 13342.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121533 restraints weight = 8413.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123627 restraints weight = 5922.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125218 restraints weight = 4550.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126437 restraints weight = 3717.156| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21460 Z= 0.123 Angle : 0.726 10.080 29032 Z= 0.355 Chirality : 0.041 0.177 3308 Planarity : 0.004 0.056 3624 Dihedral : 5.917 40.612 2808 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.17), residues: 2568 helix: -0.19 (0.14), residues: 1368 sheet: -3.37 (0.57), residues: 68 loop : -3.38 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 757 TYR 0.030 0.001 TYR B 575 PHE 0.021 0.001 PHE B 259 TRP 0.022 0.001 TRP B 742 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21460) covalent geometry : angle 0.72563 / 0.36 (29032) hydrogen bonds : bond 0.02904 / 1.88 ( 736) hydrogen bonds : angle 4.12733 / 2.77 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8756 (mptt) REVERT: C 160 HIS cc_start: 0.7520 (t-90) cc_final: 0.6956 (t70) REVERT: C 195 GLU cc_start: 0.7346 (tp30) cc_final: 0.6508 (tm-30) REVERT: C 279 GLN cc_start: 0.8606 (tp40) cc_final: 0.8232 (mm110) REVERT: C 280 LEU cc_start: 0.8546 (mm) cc_final: 0.8237 (mm) REVERT: C 282 MET cc_start: 0.8029 (tmm) cc_final: 0.7553 (tpt) REVERT: C 283 GLU cc_start: 0.8712 (mm-30) cc_final: 0.7823 (mp0) REVERT: C 355 GLU cc_start: 0.8277 (tp30) cc_final: 0.7829 (tp30) REVERT: C 387 SER cc_start: 0.8241 (t) cc_final: 0.7558 (p) REVERT: C 433 TRP cc_start: 0.8910 (t60) cc_final: 0.8625 (t60) REVERT: C 481 TRP cc_start: 0.5759 (m100) cc_final: 0.4980 (t-100) REVERT: C 542 PHE cc_start: 0.7035 (p90) cc_final: 0.6628 (p90) REVERT: C 555 MET cc_start: 0.9441 (mtt) cc_final: 0.9197 (mtt) REVERT: C 562 MET cc_start: 0.8823 (ppp) cc_final: 0.8081 (ppp) REVERT: C 589 LYS cc_start: 0.8036 (mttt) cc_final: 0.7610 (tmtt) REVERT: C 634 LYS cc_start: 0.8588 (tttt) cc_final: 0.8185 (tttt) REVERT: C 651 PRO cc_start: 0.5970 (Cg_endo) cc_final: 0.5702 (Cg_exo) REVERT: C 689 GLU cc_start: 0.8314 (tp30) cc_final: 0.8031 (tp30) REVERT: C 699 THR cc_start: 0.9023 (t) cc_final: 0.8282 (p) REVERT: C 702 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7580 (mt-10) REVERT: C 706 MET cc_start: 0.7481 (ttt) cc_final: 0.6887 (tpp) REVERT: C 758 ARG cc_start: 0.7879 (tpp80) cc_final: 0.6787 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0626 time to fit residues: 15.2009 Evaluate side-chains 154 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.198 Evaluate side-chains 175 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.198 Fit side-chains REVERT: D 121 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8746 (mptt) REVERT: D 195 GLU cc_start: 0.7444 (tp30) cc_final: 0.6673 (tm-30) REVERT: D 213 TYR cc_start: 0.7626 (p90) cc_final: 0.7046 (p90) REVERT: D 264 THR cc_start: 0.9675 (t) cc_final: 0.9455 (p) REVERT: D 281 LEU cc_start: 0.8787 (mp) cc_final: 0.8553 (mp) REVERT: D 283 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7700 (mp0) REVERT: D 284 ASN cc_start: 0.9063 (t0) cc_final: 0.8832 (t0) REVERT: D 338 ASN cc_start: 0.8320 (p0) cc_final: 0.7795 (p0) REVERT: D 355 GLU cc_start: 0.8413 (tp30) cc_final: 0.7908 (tp30) REVERT: D 359 TYR cc_start: 0.8568 (t80) cc_final: 0.8014 (t80) REVERT: D 387 SER cc_start: 0.8210 (t) cc_final: 0.7506 (p) REVERT: D 391 ASP cc_start: 0.7496 (t70) cc_final: 0.7295 (t70) REVERT: D 409 TYR cc_start: 0.7941 (m-80) cc_final: 0.6086 (m-10) REVERT: D 433 TRP cc_start: 0.9001 (t60) cc_final: 0.8766 (t60) REVERT: D 481 TRP cc_start: 0.5708 (m100) cc_final: 0.4882 (t-100) REVERT: D 555 MET cc_start: 0.9405 (mtt) cc_final: 0.9084 (mtt) REVERT: D 562 MET cc_start: 0.8796 (ppp) cc_final: 0.8044 (ppp) REVERT: D 574 MET cc_start: 0.8219 (mtp) cc_final: 0.7438 (tpp) REVERT: D 589 LYS cc_start: 0.8032 (mttt) cc_final: 0.7598 (tmtt) REVERT: D 702 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7504 (mm-30) REVERT: D 758 ARG cc_start: 0.7840 (tpp80) cc_final: 0.6838 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0584 time to fit residues: 14.0523 Evaluate side-chains 154 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 7.9990 chunk 157 optimal weight: 0.3980 chunk 153 optimal weight: 0.0870 chunk 121 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 0.0010 chunk 215 optimal weight: 10.0000 overall best weight: 1.8968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 301 HIS D 346 GLN D 580 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118171 restraints weight = 13162.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121199 restraints weight = 8304.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123262 restraints weight = 5874.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124894 restraints weight = 4535.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125923 restraints weight = 3698.241| |-----------------------------------------------------------------------------| r_work (final): 0.3617 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118106 restraints weight = 13510.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120957 restraints weight = 8794.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122996 restraints weight = 6366.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124578 restraints weight = 4991.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125687 restraints weight = 4126.179| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21460 Z= 0.126 Angle : 0.737 9.945 29032 Z= 0.365 Chirality : 0.042 0.164 3308 Planarity : 0.005 0.056 3624 Dihedral : 5.887 41.073 2808 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 0.09 % Allowed : 0.61 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.17), residues: 2568 helix: -0.16 (0.14), residues: 1368 sheet: -3.18 (0.63), residues: 68 loop : -3.39 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 327 TYR 0.020 0.001 TYR D 460 PHE 0.021 0.001 PHE A 259 TRP 0.020 0.001 TRP D 742 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21460) covalent geometry : angle 0.73693 / 0.37 (29032) hydrogen bonds : bond 0.03019 / 1.97 ( 736) hydrogen bonds : angle 4.13085 / 2.78 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8759 (mptt) REVERT: C 135 LEU cc_start: 0.8705 (tp) cc_final: 0.8465 (tp) REVERT: C 160 HIS cc_start: 0.7549 (t-90) cc_final: 0.6977 (t70) REVERT: C 195 GLU cc_start: 0.7402 (tp30) cc_final: 0.6549 (tm-30) REVERT: C 279 GLN cc_start: 0.8530 (tp40) cc_final: 0.8320 (mm110) REVERT: C 283 GLU cc_start: 0.8831 (mm-30) cc_final: 0.7910 (mp0) REVERT: C 355 GLU cc_start: 0.8270 (tp30) cc_final: 0.7932 (tp30) REVERT: C 387 SER cc_start: 0.8251 (t) cc_final: 0.7544 (p) REVERT: C 433 TRP cc_start: 0.8978 (t60) cc_final: 0.8600 (t60) REVERT: C 481 TRP cc_start: 0.5720 (m100) cc_final: 0.5009 (t-100) REVERT: C 488 MET cc_start: 0.6504 (mmm) cc_final: 0.5957 (mtp) REVERT: C 542 PHE cc_start: 0.7084 (p90) cc_final: 0.6680 (p90) REVERT: C 553 LEU cc_start: 0.9243 (tp) cc_final: 0.8947 (mm) REVERT: C 555 MET cc_start: 0.9435 (mtt) cc_final: 0.9199 (mtt) REVERT: C 574 MET cc_start: 0.7999 (mtp) cc_final: 0.7582 (ttm) REVERT: C 589 LYS cc_start: 0.7971 (mttt) cc_final: 0.7620 (tmtt) REVERT: C 651 PRO cc_start: 0.5993 (Cg_endo) cc_final: 0.5737 (Cg_exo) REVERT: C 689 GLU cc_start: 0.8164 (tp30) cc_final: 0.7937 (mm-30) REVERT: C 699 THR cc_start: 0.8999 (t) cc_final: 0.7751 (m) REVERT: C 702 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7572 (mt-10) REVERT: C 706 MET cc_start: 0.7567 (ttt) cc_final: 0.6858 (tpp) REVERT: C 732 LEU cc_start: 0.7964 (mt) cc_final: 0.7746 (mt) REVERT: C 758 ARG cc_start: 0.7891 (tpp80) cc_final: 0.6799 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0578 time to fit residues: 14.4070 Evaluate side-chains 153 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.154 Evaluate side-chains 178 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.173 Fit side-chains REVERT: D 121 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8753 (mptt) REVERT: D 195 GLU cc_start: 0.7390 (tp30) cc_final: 0.6641 (tm-30) REVERT: D 261 PHE cc_start: 0.8618 (p90) cc_final: 0.8404 (p90) REVERT: D 277 ILE cc_start: 0.9145 (tt) cc_final: 0.8907 (tt) REVERT: D 283 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8301 (mm-30) REVERT: D 327 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.6719 (ttm-80) REVERT: D 338 ASN cc_start: 0.8285 (p0) cc_final: 0.7875 (p0) REVERT: D 355 GLU cc_start: 0.8289 (tp30) cc_final: 0.7916 (tp30) REVERT: D 359 TYR cc_start: 0.8573 (t80) cc_final: 0.7994 (t80) REVERT: D 387 SER cc_start: 0.8223 (t) cc_final: 0.7495 (p) REVERT: D 391 ASP cc_start: 0.7629 (t70) cc_final: 0.7324 (t70) REVERT: D 409 TYR cc_start: 0.8025 (m-80) cc_final: 0.6159 (m-10) REVERT: D 433 TRP cc_start: 0.9025 (t60) cc_final: 0.8759 (t60) REVERT: D 481 TRP cc_start: 0.5764 (m100) cc_final: 0.4988 (t-100) REVERT: D 555 MET cc_start: 0.9410 (mtt) cc_final: 0.9095 (mtt) REVERT: D 574 MET cc_start: 0.8128 (mtp) cc_final: 0.7405 (tpp) REVERT: D 589 LYS cc_start: 0.8028 (mttt) cc_final: 0.7683 (tmtt) REVERT: D 702 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7504 (mm-30) REVERT: D 732 LEU cc_start: 0.7851 (mt) cc_final: 0.7608 (mt) REVERT: D 758 ARG cc_start: 0.7828 (tpp80) cc_final: 0.6742 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0555 time to fit residues: 13.7483 Evaluate side-chains 151 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 195 optimal weight: 0.0000 chunk 89 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 219 optimal weight: 0.0020 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116354 restraints weight = 13543.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119382 restraints weight = 8482.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121547 restraints weight = 5985.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122999 restraints weight = 4584.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124122 restraints weight = 3763.640| |-----------------------------------------------------------------------------| r_work (final): 0.3591 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117201 restraints weight = 13608.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120190 restraints weight = 8606.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122254 restraints weight = 6100.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123735 restraints weight = 4710.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124827 restraints weight = 3884.704| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21460 Z= 0.132 Angle : 0.761 9.777 29032 Z= 0.374 Chirality : 0.043 0.180 3308 Planarity : 0.004 0.057 3624 Dihedral : 5.955 41.468 2808 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.17), residues: 2568 helix: -0.15 (0.14), residues: 1372 sheet: -3.07 (0.65), residues: 68 loop : -3.48 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 757 TYR 0.020 0.002 TYR D 460 PHE 0.027 0.001 PHE D 259 TRP 0.017 0.001 TRP D 521 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21460) covalent geometry : angle 0.76096 / 0.37 (29032) hydrogen bonds : bond 0.02964 / 1.92 ( 736) hydrogen bonds : angle 4.21146 / 2.84 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.93 seconds wall clock time: 41 minutes 35.13 seconds (2495.13 seconds total)