Starting phenix.real_space_refine on Thu Mar 5 08:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvm_20493/03_2026/6pvm_20493.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvm_20493/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pvm_20493/03_2026/6pvm_20493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvm_20493/03_2026/6pvm_20493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvm_20493/03_2026/6pvm_20493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvm_20493/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.63, 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: 1.54 Conformation dependent library (CDL) restraints added in 969.0 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: 0.62 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: 2.96 Time building geometry restraints manager: 2.08 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: 0.04 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: 0.010 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 covalent geometry : bond 0.00586 (21460) covalent geometry : angle 1.18368 (29032) hydrogen bonds : bond 0.31395 ( 736) hydrogen bonds : angle 9.86982 ( 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 : 0.191 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: 0.0731 time to fit residues: 24.7038 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 : 0.204 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 : 0.167 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: 0.0709 time to fit residues: 24.1441 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 : 0.204 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 452 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS D 452 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111651 restraints weight = 12628.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114834 restraints weight = 7320.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117067 restraints weight = 4935.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118582 restraints weight = 3670.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119704 restraints weight = 2953.042| |-----------------------------------------------------------------------------| r_work (final): 0.3513 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111634 restraints weight = 12673.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114840 restraints weight = 7510.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116997 restraints weight = 5109.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118661 restraints weight = 3850.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119540 restraints weight = 3090.686| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3602 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 : 2.571 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.32 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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: -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 B 160 Details of bonding type rmsd covalent geometry : bond 0.00326 (21460) covalent geometry : angle 0.81209 (29032) hydrogen bonds : bond 0.05053 ( 736) hydrogen bonds : angle 5.51591 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8691 (mptt) REVERT: C 134 GLU cc_start: 0.8581 (mp0) cc_final: 0.8230 (tp30) REVERT: C 173 MET cc_start: 0.8599 (mtp) cc_final: 0.8256 (mtp) REVERT: C 293 ASP cc_start: 0.6932 (m-30) cc_final: 0.6639 (m-30) REVERT: C 338 ASN cc_start: 0.8541 (p0) cc_final: 0.8122 (p0) REVERT: C 342 LEU cc_start: 0.8146 (pt) cc_final: 0.7739 (pp) REVERT: C 355 GLU cc_start: 0.8448 (tp30) cc_final: 0.7708 (tp30) REVERT: C 359 TYR cc_start: 0.8430 (t80) cc_final: 0.8116 (t80) REVERT: C 542 PHE cc_start: 0.6837 (p90) cc_final: 0.6162 (p90) REVERT: C 555 MET cc_start: 0.9392 (mtt) cc_final: 0.8994 (mtt) REVERT: C 574 MET cc_start: 0.8517 (mtp) cc_final: 0.7923 (ttm) REVERT: C 578 MET cc_start: 0.8537 (tpp) cc_final: 0.8332 (mmt) REVERT: C 650 TYR cc_start: 0.4811 (m-10) cc_final: 0.4509 (t80) REVERT: C 663 ILE cc_start: 0.9160 (tp) cc_final: 0.8955 (tp) REVERT: C 673 LEU cc_start: 0.9010 (tp) cc_final: 0.8597 (tp) REVERT: C 699 THR cc_start: 0.9185 (t) cc_final: 0.8908 (m) REVERT: C 702 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7861 (mm-30) REVERT: C 705 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8351 (mttt) REVERT: C 706 MET cc_start: 0.7586 (ttt) cc_final: 0.7029 (tpp) REVERT: C 758 ARG cc_start: 0.7561 (tpp80) cc_final: 0.6637 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0637 time to fit residues: 17.7040 Evaluate side-chains 174 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.211 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 : 0.189 Fit side-chains REVERT: D 121 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8687 (mptt) REVERT: D 134 GLU cc_start: 0.8481 (mp0) cc_final: 0.8122 (tp30) REVERT: D 173 MET cc_start: 0.8603 (mtp) cc_final: 0.8247 (mtp) REVERT: D 293 ASP cc_start: 0.6903 (m-30) cc_final: 0.6616 (m-30) REVERT: D 338 ASN cc_start: 0.8482 (p0) cc_final: 0.8108 (p0) REVERT: D 342 LEU cc_start: 0.8066 (pt) cc_final: 0.7307 (pp) REVERT: D 355 GLU cc_start: 0.8431 (tp30) cc_final: 0.7718 (tp30) REVERT: D 359 TYR cc_start: 0.8426 (t80) cc_final: 0.8135 (t80) REVERT: D 555 MET cc_start: 0.9381 (mtt) cc_final: 0.8952 (mtt) REVERT: D 574 MET cc_start: 0.8504 (mtp) cc_final: 0.7804 (ttm) REVERT: D 650 TYR cc_start: 0.4828 (m-10) cc_final: 0.4506 (t80) REVERT: D 673 LEU cc_start: 0.9025 (tp) cc_final: 0.8616 (tp) REVERT: D 677 MET cc_start: 0.8394 (mmp) cc_final: 0.8051 (mtp) REVERT: D 699 THR cc_start: 0.9218 (t) cc_final: 0.8920 (m) REVERT: D 702 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 705 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8398 (mttt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0636 time to fit residues: 17.3348 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 : 0.202 ------------------------------------------------------------------------------- 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: 10.0000 chunk 216 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 211 optimal weight: 0.0870 chunk 136 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 179 optimal weight: 20.0000 chunk 4 optimal weight: 0.3980 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 GLN D 314 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114044 restraints weight = 12563.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117240 restraints weight = 7389.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119490 restraints weight = 5013.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121084 restraints weight = 3734.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122253 restraints weight = 2999.947| |-----------------------------------------------------------------------------| r_work (final): 0.3546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113186 restraints weight = 12692.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116500 restraints weight = 7401.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118763 restraints weight = 4983.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120365 restraints weight = 3706.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121432 restraints weight = 2957.441| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21460 Z= 0.129 Angle : 0.734 8.990 29032 Z= 0.367 Chirality : 0.043 0.183 3308 Planarity : 0.005 0.064 3624 Dihedral : 6.421 32.818 2808 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 16.04 % Favored : 83.64 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.88 (0.15), residues: 2568 helix: -1.59 (0.13), residues: 1300 sheet: -4.39 (0.34), residues: 76 loop : -3.66 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 295 TYR 0.022 0.001 TYR B 575 PHE 0.020 0.002 PHE B 447 TRP 0.015 0.001 TRP A 742 HIS 0.008 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00273 (21460) covalent geometry : angle 0.73416 (29032) hydrogen bonds : bond 0.03901 ( 736) hydrogen bonds : angle 4.85374 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 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: 0 poor density : 195 time to evaluate : 0.192 Fit side-chains REVERT: C 121 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8697 (mptt) REVERT: C 260 TYR cc_start: 0.8998 (t80) cc_final: 0.8702 (t80) REVERT: C 261 PHE cc_start: 0.8745 (p90) cc_final: 0.8449 (p90) REVERT: C 293 ASP cc_start: 0.6833 (m-30) cc_final: 0.6449 (m-30) REVERT: C 338 ASN cc_start: 0.8377 (p0) cc_final: 0.7756 (p0) REVERT: C 342 LEU cc_start: 0.7978 (pt) cc_final: 0.7565 (pp) REVERT: C 355 GLU cc_start: 0.8436 (tp30) cc_final: 0.7817 (tp30) REVERT: C 359 TYR cc_start: 0.8340 (t80) cc_final: 0.8108 (t80) REVERT: C 391 ASP cc_start: 0.7553 (t70) cc_final: 0.7162 (t70) REVERT: C 409 TYR cc_start: 0.8151 (m-80) cc_final: 0.7459 (m-80) REVERT: C 440 MET cc_start: 0.7228 (mmt) cc_final: 0.6977 (tpp) REVERT: C 542 PHE cc_start: 0.6882 (p90) cc_final: 0.6282 (p90) REVERT: C 555 MET cc_start: 0.9393 (mtt) cc_final: 0.9032 (mtt) REVERT: C 574 MET cc_start: 0.8432 (mtp) cc_final: 0.8013 (ttm) REVERT: C 576 SER cc_start: 0.9145 (t) cc_final: 0.8653 (p) REVERT: C 578 MET cc_start: 0.8599 (tpp) cc_final: 0.8289 (mmt) REVERT: C 589 LYS cc_start: 0.8138 (mttt) cc_final: 0.7340 (tptt) REVERT: C 625 PHE cc_start: 0.6865 (t80) cc_final: 0.6616 (t80) REVERT: C 650 TYR cc_start: 0.4596 (m-10) cc_final: 0.4348 (t80) REVERT: C 702 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 706 MET cc_start: 0.7600 (ttt) cc_final: 0.6962 (tpp) REVERT: C 758 ARG cc_start: 0.7661 (tpp80) cc_final: 0.6711 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0660 time to fit residues: 17.1438 Evaluate side-chains 165 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.195 Evaluate side-chains 194 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8694 (mptt) REVERT: D 213 TYR cc_start: 0.7371 (p90) cc_final: 0.7060 (p90) REVERT: D 260 TYR cc_start: 0.8977 (t80) cc_final: 0.8696 (t80) REVERT: D 293 ASP cc_start: 0.6801 (m-30) cc_final: 0.6304 (m-30) REVERT: D 315 ASP cc_start: 0.6938 (t70) cc_final: 0.6638 (t70) REVERT: D 319 ARG cc_start: 0.9007 (mtt180) cc_final: 0.8752 (ttm110) REVERT: D 338 ASN cc_start: 0.8197 (p0) cc_final: 0.7630 (p0) REVERT: D 342 LEU cc_start: 0.8206 (pt) cc_final: 0.7976 (pp) REVERT: D 346 GLN cc_start: 0.8862 (pt0) cc_final: 0.8488 (pt0) REVERT: D 355 GLU cc_start: 0.8320 (tp30) cc_final: 0.7691 (tp30) REVERT: D 391 ASP cc_start: 0.7659 (t70) cc_final: 0.7307 (t70) REVERT: D 501 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7445 (mm-30) REVERT: D 555 MET cc_start: 0.9391 (mtt) cc_final: 0.9021 (mtt) REVERT: D 574 MET cc_start: 0.8508 (mtp) cc_final: 0.8038 (ttm) REVERT: D 576 SER cc_start: 0.9143 (t) cc_final: 0.8660 (p) REVERT: D 589 LYS cc_start: 0.8165 (mttt) cc_final: 0.7399 (tptt) REVERT: D 650 TYR cc_start: 0.4711 (m-10) cc_final: 0.4460 (t80) REVERT: D 699 THR cc_start: 0.9304 (t) cc_final: 0.9097 (p) REVERT: D 702 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8003 (mm-30) REVERT: D 706 MET cc_start: 0.8282 (tpt) cc_final: 0.7308 (tpp) REVERT: D 758 ARG cc_start: 0.7593 (tpp80) cc_final: 0.6803 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0688 time to fit residues: 17.6140 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 : 0.186 ------------------------------------------------------------------------------- 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: 0.6980 chunk 163 optimal weight: 30.0000 chunk 226 optimal weight: 0.0270 chunk 138 optimal weight: 0.0170 chunk 229 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 139 optimal weight: 0.0570 chunk 26 optimal weight: 9.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116982 restraints weight = 12848.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120325 restraints weight = 7669.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122669 restraints weight = 5204.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124337 restraints weight = 3867.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125524 restraints weight = 3077.056| |-----------------------------------------------------------------------------| r_work (final): 0.3596 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115471 restraints weight = 12597.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118798 restraints weight = 7477.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121185 restraints weight = 5054.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122746 restraints weight = 3732.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123975 restraints weight = 2978.510| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21460 Z= 0.120 Angle : 0.691 8.926 29032 Z= 0.344 Chirality : 0.041 0.161 3308 Planarity : 0.005 0.062 3624 Dihedral : 5.973 31.096 2808 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.64 % Favored : 85.05 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.56 (0.15), residues: 2568 helix: -1.27 (0.13), residues: 1292 sheet: -4.36 (0.35), residues: 76 loop : -3.55 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 733 TYR 0.013 0.001 TYR A 564 PHE 0.020 0.001 PHE D 625 TRP 0.022 0.001 TRP C 742 HIS 0.007 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00252 (21460) covalent geometry : angle 0.69118 (29032) hydrogen bonds : bond 0.03336 ( 736) hydrogen bonds : angle 4.43506 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.182 Fit side-chains REVERT: C 121 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8712 (mptt) REVERT: C 195 GLU cc_start: 0.7919 (tp30) cc_final: 0.6991 (tm-30) REVERT: C 213 TYR cc_start: 0.7331 (p90) cc_final: 0.7000 (p90) REVERT: C 261 PHE cc_start: 0.8479 (p90) cc_final: 0.8019 (p90) REVERT: C 280 LEU cc_start: 0.8891 (tp) cc_final: 0.8687 (mm) REVERT: C 281 LEU cc_start: 0.9139 (mt) cc_final: 0.8862 (mp) REVERT: C 338 ASN cc_start: 0.8189 (p0) cc_final: 0.7501 (p0) REVERT: C 342 LEU cc_start: 0.7723 (pt) cc_final: 0.7413 (pp) REVERT: C 355 GLU cc_start: 0.8455 (tp30) cc_final: 0.7704 (tp30) REVERT: C 356 ILE cc_start: 0.9554 (tt) cc_final: 0.9300 (mm) REVERT: C 359 TYR cc_start: 0.8266 (t80) cc_final: 0.7716 (t80) REVERT: C 417 HIS cc_start: 0.8093 (p90) cc_final: 0.7856 (p90) REVERT: C 433 TRP cc_start: 0.8873 (t60) cc_final: 0.8577 (t60) REVERT: C 481 TRP cc_start: 0.5904 (m100) cc_final: 0.4955 (t-100) REVERT: C 501 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 542 PHE cc_start: 0.6944 (p90) cc_final: 0.6377 (p90) REVERT: C 555 MET cc_start: 0.9416 (mtt) cc_final: 0.9073 (mtt) REVERT: C 574 MET cc_start: 0.8372 (mtp) cc_final: 0.7862 (ttm) REVERT: C 589 LYS cc_start: 0.8090 (mttt) cc_final: 0.7400 (tmtt) REVERT: C 625 PHE cc_start: 0.6548 (t80) cc_final: 0.6038 (t80) REVERT: C 702 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 706 MET cc_start: 0.7462 (ttt) cc_final: 0.7059 (tpp) REVERT: C 722 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7257 (mtmt) REVERT: C 758 ARG cc_start: 0.7759 (tpp80) cc_final: 0.6962 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0632 time to fit residues: 16.4426 Evaluate side-chains 171 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.222 Evaluate side-chains 193 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8708 (mptt) REVERT: D 180 ASN cc_start: 0.8872 (t0) cc_final: 0.8611 (p0) REVERT: D 338 ASN cc_start: 0.8188 (p0) cc_final: 0.7602 (p0) REVERT: D 355 GLU cc_start: 0.8482 (tp30) cc_final: 0.7807 (tp30) REVERT: D 356 ILE cc_start: 0.9540 (tt) cc_final: 0.9242 (mm) REVERT: D 359 TYR cc_start: 0.8273 (t80) cc_final: 0.7749 (t80) REVERT: D 391 ASP cc_start: 0.7480 (t70) cc_final: 0.7139 (t70) REVERT: D 501 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7346 (mm-30) REVERT: D 555 MET cc_start: 0.9409 (mtt) cc_final: 0.9057 (mtt) REVERT: D 574 MET cc_start: 0.8432 (mtp) cc_final: 0.7997 (ttm) REVERT: D 589 LYS cc_start: 0.8082 (mttt) cc_final: 0.7402 (tmtt) REVERT: D 625 PHE cc_start: 0.6600 (t80) cc_final: 0.6227 (t80) REVERT: D 706 MET cc_start: 0.8296 (tpt) cc_final: 0.7015 (tpp) REVERT: D 758 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7037 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0671 time to fit residues: 17.1098 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 : 0.202 ------------------------------------------------------------------------------- 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: 6.9990 chunk 210 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 123 optimal weight: 0.9990 chunk 211 optimal weight: 0.0870 chunk 99 optimal weight: 20.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 471 HIS ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 301 HIS D 346 GLN D 647 ASN D 695 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 = 0.3778 r_free = 0.3778 target = 0.139322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116487 restraints weight = 13632.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119514 restraints weight = 8473.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121663 restraints weight = 5963.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123083 restraints weight = 4568.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124300 restraints weight = 3768.650| |-----------------------------------------------------------------------------| r_work (final): 0.3563 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111885 restraints weight = 13323.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114874 restraints weight = 8297.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117015 restraints weight = 5817.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118545 restraints weight = 4474.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119587 restraints weight = 3658.108| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21460 Z= 0.137 Angle : 0.703 8.938 29032 Z= 0.355 Chirality : 0.042 0.144 3308 Planarity : 0.005 0.056 3624 Dihedral : 6.013 30.622 2808 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.47 % Allowed : 16.20 % Favored : 83.33 % Rotamer: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.36 (0.15), residues: 2568 helix: -1.13 (0.13), residues: 1316 sheet: -4.06 (0.37), residues: 76 loop : -3.48 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 733 TYR 0.013 0.001 TYR C 382 PHE 0.022 0.001 PHE D 447 TRP 0.019 0.001 TRP A 742 HIS 0.010 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00299 (21460) covalent geometry : angle 0.70311 (29032) hydrogen bonds : bond 0.03268 ( 736) hydrogen bonds : angle 4.52988 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.195 Fit side-chains REVERT: C 121 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8748 (mptt) REVERT: C 135 LEU cc_start: 0.8807 (tp) cc_final: 0.8571 (tp) REVERT: C 159 MET cc_start: 0.7661 (mtp) cc_final: 0.7392 (mtp) REVERT: C 261 PHE cc_start: 0.8425 (p90) cc_final: 0.8010 (p90) REVERT: C 281 LEU cc_start: 0.9120 (mt) cc_final: 0.8917 (mp) REVERT: C 338 ASN cc_start: 0.8263 (p0) cc_final: 0.7562 (p0) REVERT: C 342 LEU cc_start: 0.7603 (pt) cc_final: 0.7278 (pp) REVERT: C 355 GLU cc_start: 0.8398 (tp30) cc_final: 0.7803 (tp30) REVERT: C 356 ILE cc_start: 0.9599 (tt) cc_final: 0.9331 (mm) REVERT: C 481 TRP cc_start: 0.5815 (m100) cc_final: 0.4932 (t-100) REVERT: C 542 PHE cc_start: 0.6921 (p90) cc_final: 0.6332 (p90) REVERT: C 552 VAL cc_start: 0.9626 (p) cc_final: 0.9424 (p) REVERT: C 555 MET cc_start: 0.9425 (mtt) cc_final: 0.9099 (mtt) REVERT: C 574 MET cc_start: 0.8302 (mtp) cc_final: 0.7811 (ttm) REVERT: C 589 LYS cc_start: 0.8096 (mttt) cc_final: 0.7514 (tmtt) REVERT: C 625 PHE cc_start: 0.6578 (t80) cc_final: 0.6233 (t80) REVERT: C 630 LEU cc_start: 0.9377 (mm) cc_final: 0.9160 (mm) REVERT: C 706 MET cc_start: 0.7801 (ttt) cc_final: 0.7035 (tpp) REVERT: C 722 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7661 (mtmt) REVERT: C 758 ARG cc_start: 0.7621 (tpp80) cc_final: 0.6879 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.0588 time to fit residues: 15.3589 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 : 0.195 Evaluate side-chains 185 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.192 Fit side-chains REVERT: D 121 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8714 (mptt) REVERT: D 173 MET cc_start: 0.8479 (mtp) cc_final: 0.8257 (mtp) REVERT: D 281 LEU cc_start: 0.9052 (mp) cc_final: 0.8791 (mp) REVERT: D 338 ASN cc_start: 0.8165 (p0) cc_final: 0.7640 (p0) REVERT: D 355 GLU cc_start: 0.8485 (tp30) cc_final: 0.7912 (tp30) REVERT: D 356 ILE cc_start: 0.9594 (tt) cc_final: 0.9328 (mm) REVERT: D 391 ASP cc_start: 0.7797 (t70) cc_final: 0.7347 (t70) REVERT: D 481 TRP cc_start: 0.5780 (m100) cc_final: 0.4842 (t-100) REVERT: D 552 VAL cc_start: 0.9650 (p) cc_final: 0.9437 (p) REVERT: D 555 MET cc_start: 0.9413 (mtt) cc_final: 0.9080 (mtt) REVERT: D 574 MET cc_start: 0.8478 (mtp) cc_final: 0.7995 (ttm) REVERT: D 589 LYS cc_start: 0.8033 (mttt) cc_final: 0.7480 (tmtt) REVERT: D 625 PHE cc_start: 0.6505 (t80) cc_final: 0.5995 (t80) REVERT: D 702 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 758 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7095 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0611 time to fit residues: 15.2053 Evaluate side-chains 156 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 0.0070 chunk 141 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 251 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 695 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN D 301 HIS D 346 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119757 restraints weight = 13549.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122877 restraints weight = 8497.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125071 restraints weight = 5979.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126531 restraints weight = 4577.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127703 restraints weight = 3758.350| |-----------------------------------------------------------------------------| r_work (final): 0.3585 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118474 restraints weight = 12738.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121643 restraints weight = 7649.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123840 restraints weight = 5243.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125523 restraints weight = 3931.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126663 restraints weight = 3132.696| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21460 Z= 0.118 Angle : 0.708 8.938 29032 Z= 0.346 Chirality : 0.041 0.136 3308 Planarity : 0.004 0.055 3624 Dihedral : 5.798 30.024 2808 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.34 % Favored : 84.35 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.39 (0.15), residues: 2568 helix: -1.19 (0.13), residues: 1332 sheet: -4.13 (0.40), residues: 76 loop : -3.47 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 733 TYR 0.019 0.001 TYR C 650 PHE 0.017 0.001 PHE D 625 TRP 0.021 0.001 TRP A 742 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00252 (21460) covalent geometry : angle 0.70814 (29032) hydrogen bonds : bond 0.03208 ( 736) hydrogen bonds : angle 4.37366 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: C 121 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8718 (mptt) REVERT: C 135 LEU cc_start: 0.8770 (tp) cc_final: 0.8553 (tp) REVERT: C 159 MET cc_start: 0.7575 (mtp) cc_final: 0.7309 (mtp) REVERT: C 338 ASN cc_start: 0.8180 (p0) cc_final: 0.7495 (p0) REVERT: C 355 GLU cc_start: 0.8363 (tp30) cc_final: 0.7852 (tp30) REVERT: C 356 ILE cc_start: 0.9546 (tt) cc_final: 0.9267 (mm) REVERT: C 387 SER cc_start: 0.8528 (t) cc_final: 0.8040 (p) REVERT: C 409 TYR cc_start: 0.8065 (m-10) cc_final: 0.6473 (m-10) REVERT: C 433 TRP cc_start: 0.8874 (t60) cc_final: 0.8472 (t60) REVERT: C 481 TRP cc_start: 0.5809 (m100) cc_final: 0.4900 (t-100) REVERT: C 485 LEU cc_start: 0.8068 (mp) cc_final: 0.7711 (mt) REVERT: C 542 PHE cc_start: 0.6995 (p90) cc_final: 0.6403 (p90) REVERT: C 555 MET cc_start: 0.9465 (mtt) cc_final: 0.9204 (mtt) REVERT: C 574 MET cc_start: 0.8203 (mtp) cc_final: 0.7774 (ttm) REVERT: C 589 LYS cc_start: 0.7976 (mttt) cc_final: 0.7483 (tmtt) REVERT: C 630 LEU cc_start: 0.9345 (mm) cc_final: 0.9114 (mm) REVERT: C 702 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7539 (mm-30) REVERT: C 706 MET cc_start: 0.7695 (ttt) cc_final: 0.6823 (tpp) REVERT: C 722 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7168 (mtmt) REVERT: C 730 LEU cc_start: 0.8502 (mp) cc_final: 0.8239 (mp) REVERT: C 733 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6776 (mtp85) REVERT: C 758 ARG cc_start: 0.7877 (tpp80) cc_final: 0.6923 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0613 time to fit residues: 15.4660 Evaluate side-chains 156 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.196 Evaluate side-chains 183 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8706 (mptt) REVERT: D 135 LEU cc_start: 0.8811 (tp) cc_final: 0.8590 (tp) REVERT: D 284 ASN cc_start: 0.9117 (t0) cc_final: 0.8815 (t0) REVERT: D 338 ASN cc_start: 0.8078 (p0) cc_final: 0.7464 (p0) REVERT: D 355 GLU cc_start: 0.8497 (tp30) cc_final: 0.7823 (tp30) REVERT: D 356 ILE cc_start: 0.9524 (tt) cc_final: 0.9243 (mm) REVERT: D 391 ASP cc_start: 0.7407 (t70) cc_final: 0.7034 (t70) REVERT: D 409 TYR cc_start: 0.8154 (m-10) cc_final: 0.6499 (m-10) REVERT: D 439 TYR cc_start: 0.7628 (m-80) cc_final: 0.7359 (m-10) REVERT: D 481 TRP cc_start: 0.5749 (m100) cc_final: 0.4897 (t-100) REVERT: D 555 MET cc_start: 0.9431 (mtt) cc_final: 0.9116 (mtt) REVERT: D 562 MET cc_start: 0.8887 (ppp) cc_final: 0.8015 (ppp) REVERT: D 567 ARG cc_start: 0.8476 (mtt180) cc_final: 0.7886 (ptp-110) REVERT: D 574 MET cc_start: 0.8252 (mtp) cc_final: 0.7690 (ttm) REVERT: D 589 LYS cc_start: 0.7993 (mttt) cc_final: 0.7597 (tmtt) REVERT: D 625 PHE cc_start: 0.6263 (t80) cc_final: 0.5913 (t80) REVERT: D 702 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 758 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7103 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0594 time to fit residues: 14.7700 Evaluate side-chains 159 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 1.9990 chunk 217 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 85 optimal weight: 0.0470 chunk 142 optimal weight: 0.0030 chunk 158 optimal weight: 10.0000 chunk 183 optimal weight: 0.0980 chunk 246 optimal weight: 9.9990 chunk 91 optimal weight: 0.0970 chunk 92 optimal weight: 9.9990 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 426 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122965 restraints weight = 13541.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126043 restraints weight = 8511.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128234 restraints weight = 5996.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129800 restraints weight = 4590.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130835 restraints weight = 3747.609| |-----------------------------------------------------------------------------| r_work (final): 0.3643 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118506 restraints weight = 13436.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121794 restraints weight = 8182.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124190 restraints weight = 5660.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125790 restraints weight = 4263.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127036 restraints weight = 3443.628| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21460 Z= 0.117 Angle : 0.694 8.963 29032 Z= 0.340 Chirality : 0.041 0.152 3308 Planarity : 0.004 0.054 3624 Dihedral : 5.636 29.037 2808 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.73 % Favored : 83.96 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.16), residues: 2568 helix: -1.17 (0.13), residues: 1352 sheet: -4.22 (0.40), residues: 76 loop : -3.48 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 733 TYR 0.016 0.001 TYR B 650 PHE 0.015 0.001 PHE B 625 TRP 0.016 0.001 TRP D 331 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00251 (21460) covalent geometry : angle 0.69407 (29032) hydrogen bonds : bond 0.02932 ( 736) hydrogen bonds : angle 4.26733 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8710 (mptt) REVERT: C 135 LEU cc_start: 0.8747 (tp) cc_final: 0.8527 (tp) REVERT: C 159 MET cc_start: 0.7647 (mtp) cc_final: 0.7356 (mtp) REVERT: C 195 GLU cc_start: 0.7482 (tp30) cc_final: 0.6509 (tm-30) REVERT: C 281 LEU cc_start: 0.8860 (mp) cc_final: 0.8654 (mp) REVERT: C 284 ASN cc_start: 0.9103 (t0) cc_final: 0.8814 (t0) REVERT: C 338 ASN cc_start: 0.8140 (p0) cc_final: 0.7667 (p0) REVERT: C 355 GLU cc_start: 0.8383 (tp30) cc_final: 0.7871 (tp30) REVERT: C 387 SER cc_start: 0.8369 (t) cc_final: 0.7769 (p) REVERT: C 409 TYR cc_start: 0.7988 (m-10) cc_final: 0.6357 (m-10) REVERT: C 433 TRP cc_start: 0.8868 (t60) cc_final: 0.8543 (t60) REVERT: C 481 TRP cc_start: 0.5751 (m100) cc_final: 0.4919 (t-100) REVERT: C 485 LEU cc_start: 0.7844 (mp) cc_final: 0.7503 (mt) REVERT: C 542 PHE cc_start: 0.7033 (p90) cc_final: 0.6571 (p90) REVERT: C 555 MET cc_start: 0.9477 (mtt) cc_final: 0.9184 (mtt) REVERT: C 574 MET cc_start: 0.8141 (mtp) cc_final: 0.7631 (ttm) REVERT: C 589 LYS cc_start: 0.7931 (mttt) cc_final: 0.7499 (tmtt) REVERT: C 630 LEU cc_start: 0.9258 (mm) cc_final: 0.9023 (mm) REVERT: C 699 THR cc_start: 0.8994 (t) cc_final: 0.8654 (m) REVERT: C 702 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7575 (mm-30) REVERT: C 706 MET cc_start: 0.7501 (ttt) cc_final: 0.6915 (tpp) REVERT: C 722 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7142 (ttmt) REVERT: C 758 ARG cc_start: 0.7925 (tpp80) cc_final: 0.6862 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0600 time to fit residues: 14.8030 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 : 0.205 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 : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8710 (mptt) REVERT: D 135 LEU cc_start: 0.8751 (tp) cc_final: 0.8505 (tp) REVERT: D 159 MET cc_start: 0.7575 (mtp) cc_final: 0.7345 (mtp) REVERT: D 195 GLU cc_start: 0.7500 (tp30) cc_final: 0.6639 (tm-30) REVERT: D 260 TYR cc_start: 0.8801 (t80) cc_final: 0.8339 (t80) REVERT: D 283 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7794 (mp0) REVERT: D 293 ASP cc_start: 0.6926 (m-30) cc_final: 0.4778 (m-30) REVERT: D 338 ASN cc_start: 0.8053 (p0) cc_final: 0.7615 (p0) REVERT: D 355 GLU cc_start: 0.8352 (tp30) cc_final: 0.7760 (tp30) REVERT: D 387 SER cc_start: 0.8356 (t) cc_final: 0.7767 (p) REVERT: D 409 TYR cc_start: 0.8131 (m-10) cc_final: 0.6247 (m-10) REVERT: D 481 TRP cc_start: 0.5659 (m100) cc_final: 0.4866 (t-100) REVERT: D 555 MET cc_start: 0.9412 (mtt) cc_final: 0.9113 (mtt) REVERT: D 562 MET cc_start: 0.8773 (ppp) cc_final: 0.8028 (ppp) REVERT: D 574 MET cc_start: 0.8166 (mtp) cc_final: 0.7493 (ttm) REVERT: D 589 LYS cc_start: 0.7956 (mttt) cc_final: 0.7552 (tmtt) REVERT: D 693 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7689 (ttm170) REVERT: D 702 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7539 (mm-30) REVERT: D 758 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7074 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0703 time to fit residues: 16.6003 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 : 0.204 ------------------------------------------------------------------------------- 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: 6.9990 chunk 232 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 107 optimal weight: 0.0040 chunk 156 optimal weight: 0.0470 chunk 169 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 overall best weight: 2.4894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 301 HIS D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120447 restraints weight = 13776.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123437 restraints weight = 8756.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125565 restraints weight = 6259.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127081 restraints weight = 4859.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128076 restraints weight = 4020.218| |-----------------------------------------------------------------------------| r_work (final): 0.3609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115396 restraints weight = 13235.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118807 restraints weight = 8077.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121150 restraints weight = 5558.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122834 restraints weight = 4183.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123930 restraints weight = 3363.521| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6086 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= 0.120 Angle : 0.706 8.909 29032 Z= 0.346 Chirality : 0.041 0.148 3308 Planarity : 0.004 0.054 3624 Dihedral : 5.593 28.873 2808 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.03 % Favored : 84.66 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.16), residues: 2568 helix: -1.10 (0.13), residues: 1376 sheet: -4.20 (0.43), residues: 76 loop : -3.50 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 733 TYR 0.026 0.001 TYR B 460 PHE 0.012 0.001 PHE C 250 TRP 0.015 0.001 TRP D 742 HIS 0.008 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00266 (21460) covalent geometry : angle 0.70647 (29032) hydrogen bonds : bond 0.02970 ( 736) hydrogen bonds : angle 4.20586 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8759 (mptt) REVERT: C 135 LEU cc_start: 0.8801 (tp) cc_final: 0.8571 (tp) REVERT: C 195 GLU cc_start: 0.7443 (tp30) cc_final: 0.6481 (tm-30) REVERT: C 279 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8332 (mm-40) REVERT: C 281 LEU cc_start: 0.8846 (mp) cc_final: 0.8587 (mp) REVERT: C 282 MET cc_start: 0.7581 (tpp) cc_final: 0.7216 (tmm) REVERT: C 283 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7658 (mp0) REVERT: C 284 ASN cc_start: 0.9044 (t0) cc_final: 0.8838 (t0) REVERT: C 327 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6120 (ttm-80) REVERT: C 338 ASN cc_start: 0.8048 (p0) cc_final: 0.7643 (p0) REVERT: C 355 GLU cc_start: 0.8371 (tp30) cc_final: 0.7954 (tp30) REVERT: C 387 SER cc_start: 0.8473 (t) cc_final: 0.7896 (p) REVERT: C 409 TYR cc_start: 0.8071 (m-10) cc_final: 0.6994 (m-10) REVERT: C 433 TRP cc_start: 0.9001 (t60) cc_final: 0.8641 (t60) REVERT: C 481 TRP cc_start: 0.5770 (m100) cc_final: 0.5006 (t-100) REVERT: C 485 LEU cc_start: 0.8004 (mp) cc_final: 0.7705 (mt) REVERT: C 542 PHE cc_start: 0.6982 (p90) cc_final: 0.6538 (p90) REVERT: C 555 MET cc_start: 0.9457 (mtt) cc_final: 0.9202 (mtt) REVERT: C 574 MET cc_start: 0.8068 (mtp) cc_final: 0.7525 (ttm) REVERT: C 589 LYS cc_start: 0.7974 (mttt) cc_final: 0.7556 (tmtt) REVERT: C 699 THR cc_start: 0.9012 (t) cc_final: 0.8679 (m) REVERT: C 702 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7701 (mm-30) REVERT: C 706 MET cc_start: 0.7677 (ttt) cc_final: 0.6902 (tpp) REVERT: C 722 LYS cc_start: 0.7667 (mtmt) cc_final: 0.7162 (mttt) REVERT: C 733 ARG cc_start: 0.6812 (mtp-110) cc_final: 0.6348 (mtm180) REVERT: C 758 ARG cc_start: 0.7906 (tpp80) cc_final: 0.6867 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0633 time to fit residues: 14.9634 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 : 0.215 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 : 0.243 Fit side-chains revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8706 (mptt) REVERT: D 135 LEU cc_start: 0.8838 (tp) cc_final: 0.8608 (tp) REVERT: D 159 MET cc_start: 0.7544 (mtp) cc_final: 0.7299 (mtp) REVERT: D 260 TYR cc_start: 0.8945 (t80) cc_final: 0.8665 (t80) REVERT: D 282 MET cc_start: 0.7880 (tmm) cc_final: 0.7632 (tpp) REVERT: D 283 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7776 (mp0) REVERT: D 284 ASN cc_start: 0.9190 (t0) cc_final: 0.8915 (t0) REVERT: D 293 ASP cc_start: 0.6620 (m-30) cc_final: 0.5813 (m-30) REVERT: D 338 ASN cc_start: 0.8339 (p0) cc_final: 0.8010 (p0) REVERT: D 342 LEU cc_start: 0.8254 (pp) cc_final: 0.7948 (pp) REVERT: D 355 GLU cc_start: 0.8508 (tp30) cc_final: 0.7893 (tp30) REVERT: D 387 SER cc_start: 0.8427 (t) cc_final: 0.7678 (p) REVERT: D 409 TYR cc_start: 0.8170 (m-10) cc_final: 0.6405 (m-10) REVERT: D 417 HIS cc_start: 0.8367 (p-80) cc_final: 0.8122 (p-80) REVERT: D 481 TRP cc_start: 0.5797 (m100) cc_final: 0.4976 (t-100) REVERT: D 555 MET cc_start: 0.9470 (mtt) cc_final: 0.9181 (mtt) REVERT: D 562 MET cc_start: 0.8945 (ppp) cc_final: 0.8093 (ppp) REVERT: D 574 MET cc_start: 0.8140 (mtp) cc_final: 0.7645 (ttm) REVERT: D 589 LYS cc_start: 0.7837 (mttt) cc_final: 0.7450 (tmtt) REVERT: D 702 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7591 (mm-30) REVERT: D 758 ARG cc_start: 0.8012 (tpp80) cc_final: 0.6928 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0597 time to fit residues: 14.3421 Evaluate side-chains 144 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 6.9990 chunk 221 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 153 optimal weight: 0.1980 chunk 205 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 301 HIS D 346 GLN D 671 ASN D 695 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 = 0.3801 r_free = 0.3801 target = 0.140814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119368 restraints weight = 13116.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122425 restraints weight = 7889.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124617 restraints weight = 5408.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126182 restraints weight = 4052.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127321 restraints weight = 3247.070| |-----------------------------------------------------------------------------| r_work (final): 0.3627 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115906 restraints weight = 13366.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119188 restraints weight = 8081.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121518 restraints weight = 5565.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123049 restraints weight = 4188.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124239 restraints weight = 3389.622| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21460 Z= 0.120 Angle : 0.710 8.908 29032 Z= 0.348 Chirality : 0.042 0.205 3308 Planarity : 0.004 0.056 3624 Dihedral : 5.656 28.699 2808 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.11 % Favored : 84.58 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.16), residues: 2568 helix: -0.94 (0.14), residues: 1348 sheet: -4.14 (0.45), residues: 76 loop : -3.49 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 733 TYR 0.020 0.002 TYR B 382 PHE 0.024 0.001 PHE D 625 TRP 0.015 0.001 TRP D 742 HIS 0.009 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00264 (21460) covalent geometry : angle 0.71040 (29032) hydrogen bonds : bond 0.02970 ( 736) hydrogen bonds : angle 4.22199 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8761 (mptt) REVERT: C 135 LEU cc_start: 0.8829 (tp) cc_final: 0.8569 (tp) REVERT: C 195 GLU cc_start: 0.7451 (tp30) cc_final: 0.6512 (tm-30) REVERT: C 277 ILE cc_start: 0.9204 (tt) cc_final: 0.8999 (tt) REVERT: C 281 LEU cc_start: 0.8841 (mp) cc_final: 0.8613 (mp) REVERT: C 284 ASN cc_start: 0.9080 (t0) cc_final: 0.8871 (t0) REVERT: C 327 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.7046 (tpp-160) REVERT: C 338 ASN cc_start: 0.8226 (p0) cc_final: 0.7680 (p0) REVERT: C 355 GLU cc_start: 0.8430 (tp30) cc_final: 0.7892 (tp30) REVERT: C 387 SER cc_start: 0.8453 (t) cc_final: 0.7848 (p) REVERT: C 409 TYR cc_start: 0.8154 (m-10) cc_final: 0.7033 (m-10) REVERT: C 433 TRP cc_start: 0.8976 (t60) cc_final: 0.8607 (t60) REVERT: C 481 TRP cc_start: 0.5795 (m100) cc_final: 0.4962 (t-100) REVERT: C 485 LEU cc_start: 0.7950 (mp) cc_final: 0.7678 (mt) REVERT: C 542 PHE cc_start: 0.6992 (p90) cc_final: 0.6524 (p90) REVERT: C 555 MET cc_start: 0.9486 (mtt) cc_final: 0.9245 (mtt) REVERT: C 574 MET cc_start: 0.8097 (mtp) cc_final: 0.7864 (mtp) REVERT: C 589 LYS cc_start: 0.8009 (mttt) cc_final: 0.7622 (tmtt) REVERT: C 699 THR cc_start: 0.8970 (t) cc_final: 0.8594 (m) REVERT: C 702 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7716 (mm-30) REVERT: C 706 MET cc_start: 0.7431 (ttt) cc_final: 0.6826 (tpp) REVERT: C 758 ARG cc_start: 0.7946 (tpp80) cc_final: 0.6924 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0603 time to fit residues: 14.3490 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 : 0.210 Evaluate side-chains 177 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8733 (mptt) REVERT: D 135 LEU cc_start: 0.8850 (tp) cc_final: 0.8614 (tp) REVERT: D 283 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7656 (mp0) REVERT: D 284 ASN cc_start: 0.9209 (t0) cc_final: 0.8873 (t0) REVERT: D 338 ASN cc_start: 0.8438 (p0) cc_final: 0.8054 (p0) REVERT: D 342 LEU cc_start: 0.8168 (pp) cc_final: 0.7890 (pp) REVERT: D 355 GLU cc_start: 0.8476 (tp30) cc_final: 0.7869 (tp30) REVERT: D 387 SER cc_start: 0.8319 (t) cc_final: 0.7616 (p) REVERT: D 409 TYR cc_start: 0.8225 (m-10) cc_final: 0.6438 (m-10) REVERT: D 417 HIS cc_start: 0.8277 (p-80) cc_final: 0.8020 (p-80) REVERT: D 481 TRP cc_start: 0.5652 (m100) cc_final: 0.4742 (t-100) REVERT: D 553 LEU cc_start: 0.9205 (tp) cc_final: 0.8967 (mm) REVERT: D 555 MET cc_start: 0.9462 (mtt) cc_final: 0.9144 (mtt) REVERT: D 574 MET cc_start: 0.8119 (mtp) cc_final: 0.7857 (mtp) REVERT: D 589 LYS cc_start: 0.7858 (mttt) cc_final: 0.7464 (tmtt) REVERT: D 702 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7605 (mm-30) REVERT: D 758 ARG cc_start: 0.8006 (tpp80) cc_final: 0.6909 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0596 time to fit residues: 14.3444 Evaluate side-chains 144 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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: 0.0970 chunk 157 optimal weight: 0.0170 chunk 153 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 29 optimal weight: 0.0170 chunk 125 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 215 optimal weight: 0.5980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 671 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 GLN D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.144991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121920 restraints weight = 13178.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124914 restraints weight = 8450.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127049 restraints weight = 6042.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128562 restraints weight = 4677.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129696 restraints weight = 3860.435| |-----------------------------------------------------------------------------| r_work (final): 0.3668 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120919 restraints weight = 13269.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124302 restraints weight = 8203.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126701 restraints weight = 5725.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128404 restraints weight = 4343.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129561 restraints weight = 3503.258| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6545 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= 0.123 Angle : 0.730 9.220 29032 Z= 0.353 Chirality : 0.042 0.166 3308 Planarity : 0.005 0.056 3624 Dihedral : 5.533 29.271 2808 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.19 % Favored : 84.50 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.15), residues: 2568 helix: -1.15 (0.13), residues: 1364 sheet: -4.26 (0.45), residues: 76 loop : -3.63 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 733 TYR 0.014 0.001 TYR B 650 PHE 0.019 0.001 PHE C 259 TRP 0.018 0.001 TRP D 742 HIS 0.004 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00260 (21460) covalent geometry : angle 0.72995 (29032) hydrogen bonds : bond 0.02851 ( 736) hydrogen bonds : angle 4.19859 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8763 (mptt) REVERT: C 135 LEU cc_start: 0.8780 (tp) cc_final: 0.8507 (tp) REVERT: C 195 GLU cc_start: 0.7406 (tp30) cc_final: 0.6457 (tm-30) REVERT: C 279 GLN cc_start: 0.8827 (tp40) cc_final: 0.8451 (mm110) REVERT: C 281 LEU cc_start: 0.8818 (mp) cc_final: 0.8562 (mp) REVERT: C 338 ASN cc_start: 0.7937 (p0) cc_final: 0.7473 (p0) REVERT: C 355 GLU cc_start: 0.8274 (tp30) cc_final: 0.7803 (tp30) REVERT: C 387 SER cc_start: 0.8360 (t) cc_final: 0.7647 (p) REVERT: C 433 TRP cc_start: 0.8906 (t60) cc_final: 0.8673 (t60) REVERT: C 481 TRP cc_start: 0.5749 (m100) cc_final: 0.4996 (t-100) REVERT: C 542 PHE cc_start: 0.7014 (p90) cc_final: 0.6550 (p90) REVERT: C 553 LEU cc_start: 0.9079 (tp) cc_final: 0.8815 (mm) REVERT: C 555 MET cc_start: 0.9421 (mtt) cc_final: 0.9170 (mtt) REVERT: C 574 MET cc_start: 0.7999 (mtp) cc_final: 0.7767 (mtp) REVERT: C 699 THR cc_start: 0.8981 (t) cc_final: 0.7458 (m) REVERT: C 702 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7627 (mt-10) REVERT: C 706 MET cc_start: 0.7397 (ttt) cc_final: 0.6748 (tpp) REVERT: C 758 ARG cc_start: 0.7812 (tpp80) cc_final: 0.6818 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0555 time to fit residues: 13.5849 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 : 0.204 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 : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8712 (mptt) REVERT: D 135 LEU cc_start: 0.8767 (tp) cc_final: 0.8503 (tp) REVERT: D 174 LYS cc_start: 0.7950 (tptm) cc_final: 0.7737 (tptm) REVERT: D 327 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6556 (ttm-80) REVERT: D 338 ASN cc_start: 0.8194 (p0) cc_final: 0.7948 (p0) REVERT: D 345 LEU cc_start: 0.9220 (tp) cc_final: 0.8973 (tp) REVERT: D 355 GLU cc_start: 0.8316 (tp30) cc_final: 0.7725 (tp30) REVERT: D 387 SER cc_start: 0.8202 (t) cc_final: 0.7363 (p) REVERT: D 409 TYR cc_start: 0.8135 (m-10) cc_final: 0.6329 (m-10) REVERT: D 417 HIS cc_start: 0.8408 (p-80) cc_final: 0.8115 (p-80) REVERT: D 433 TRP cc_start: 0.8939 (t60) cc_final: 0.8612 (t60) REVERT: D 481 TRP cc_start: 0.5796 (m100) cc_final: 0.4989 (t-100) REVERT: D 553 LEU cc_start: 0.9115 (tp) cc_final: 0.8893 (mm) REVERT: D 555 MET cc_start: 0.9351 (mtt) cc_final: 0.9138 (mtt) REVERT: D 574 MET cc_start: 0.8023 (mtp) cc_final: 0.7791 (mtp) REVERT: D 589 LYS cc_start: 0.7945 (mttt) cc_final: 0.7587 (tmtt) REVERT: D 702 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 758 ARG cc_start: 0.7951 (tpp80) cc_final: 0.6908 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0601 time to fit residues: 14.5776 Evaluate side-chains 145 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 9.9990 chunk 177 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 52 optimal weight: 0.0370 chunk 195 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 154 optimal weight: 0.1980 chunk 191 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 overall best weight: 2.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 GLN C 301 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 301 HIS D 313 GLN D 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118511 restraints weight = 13591.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121548 restraints weight = 8583.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123719 restraints weight = 6086.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125174 restraints weight = 4685.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126398 restraints weight = 3863.217| |-----------------------------------------------------------------------------| r_work (final): 0.3625 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117991 restraints weight = 12915.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121103 restraints weight = 7910.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123391 restraints weight = 5509.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124999 restraints weight = 4145.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126099 restraints weight = 3325.700| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21460 Z= 0.122 Angle : 0.719 9.081 29032 Z= 0.351 Chirality : 0.042 0.201 3308 Planarity : 0.004 0.054 3624 Dihedral : 5.491 29.198 2808 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.42 % Favored : 84.27 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.16), residues: 2568 helix: -0.91 (0.14), residues: 1360 sheet: -4.27 (0.43), residues: 76 loop : -3.58 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 733 TYR 0.024 0.002 TYR A 382 PHE 0.017 0.001 PHE B 447 TRP 0.015 0.001 TRP B 521 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00278 (21460) covalent geometry : angle 0.71917 (29032) hydrogen bonds : bond 0.02831 ( 736) hydrogen bonds : angle 4.15403 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.02 seconds wall clock time: 39 minutes 51.48 seconds (2391.48 seconds total)