Starting phenix.real_space_refine on Fri Aug 7 16:37:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lu_77145/08_2026/13lu_77145.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lu_77145/08_2026/13lu_77145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lu_77145/08_2026/13lu_77145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lu_77145/08_2026/13lu_77145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lu_77145/08_2026/13lu_77145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lu_77145/08_2026/13lu_77145.map" } resolution = 2.49 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= 0.014 sd= 0.244 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 14548 2.51 5 N 3392 2.21 5 O 4037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22137 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5080 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5080 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5080 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5080 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 420 Unusual residues: {' NA': 4, 'POV': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 4.78, per 1000 atoms: 0.22 Number of scatterers: 22137 At special positions: 0 Unit cell: (152.638, 152.638, 131.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 32 15.00 Na 4 11.00 O 4037 8.00 N 3392 7.00 C 14548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.04 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 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: 1.68 Conformation dependent library (CDL) restraints added in 945.8 milliseconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 64.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.819A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.514A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.627A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.520A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 Processing helix 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 Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.542A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 4.203A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.806A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.713A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.540A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.577A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.640A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.597A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.818A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.514A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.628A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.520A pdb=" N LEU B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 Processing helix 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 Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.542A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 4.203A pdb=" N VAL B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.807A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.713A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.539A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.577A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.640A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.598A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.818A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.514A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.627A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 236 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.521A pdb=" N LEU C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 Processing helix 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 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.542A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 4.204A pdb=" N VAL C 525 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.807A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.714A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.539A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.639A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 705 removed outlier: 3.597A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.819A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.515A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.626A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 236 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.520A pdb=" N LEU D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 Processing helix 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 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.543A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 494 " --> pdb=" O VAL D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 4.203A pdb=" N VAL D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.807A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.713A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.539A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.641A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 705 removed outlier: 3.598A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.014A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.014A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.014A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.013A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3520 1.32 - 1.45: 5580 1.45 - 1.57: 13020 1.57 - 1.69: 64 1.69 - 1.81: 204 Bond restraints: 22388 Sorted by residual: bond pdb=" O12 POV B1106 " pdb=" P POV B1106 " ideal model delta sigma weight residual 1.657 1.588 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O12 POV A1104 " pdb=" P POV A1104 " ideal model delta sigma weight residual 1.657 1.588 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O12 POV C1105 " pdb=" P POV C1105 " ideal model delta sigma weight residual 1.657 1.589 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O12 POV D1107 " pdb=" P POV D1107 " ideal model delta sigma weight residual 1.657 1.589 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O12 POV D1105 " pdb=" P POV D1105 " ideal model delta sigma weight residual 1.657 1.592 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 22383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 28388 1.81 - 3.62: 1300 3.62 - 5.43: 165 5.43 - 7.24: 75 7.24 - 9.05: 32 Bond angle restraints: 29960 Sorted by residual: angle pdb=" C GLN B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 121.90 113.45 8.45 1.26e+00 6.30e-01 4.50e+01 angle pdb=" C GLN C 313 " pdb=" N ASN C 314 " pdb=" CA ASN C 314 " ideal model delta sigma weight residual 121.90 113.50 8.40 1.26e+00 6.30e-01 4.45e+01 angle pdb=" C GLN D 313 " pdb=" N ASN D 314 " pdb=" CA ASN D 314 " ideal model delta sigma weight residual 121.90 113.50 8.40 1.26e+00 6.30e-01 4.44e+01 angle pdb=" C GLN A 313 " pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 121.90 113.50 8.40 1.26e+00 6.30e-01 4.44e+01 angle pdb=" C GLN D 346 " pdb=" N LEU D 347 " pdb=" CA LEU D 347 " ideal model delta sigma weight residual 120.28 127.01 -6.73 1.44e+00 4.82e-01 2.19e+01 ... (remaining 29955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 13274 35.17 - 70.35: 390 70.35 - 105.52: 68 105.52 - 140.69: 33 140.69 - 175.86: 15 Dihedral angle restraints: 13780 sinusoidal: 6420 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 -176.56 -90.44 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 -176.56 -90.44 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 -176.57 -90.43 1 1.00e+01 1.00e-02 9.67e+01 ... (remaining 13777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2849 0.072 - 0.145: 327 0.145 - 0.217: 44 0.217 - 0.289: 4 0.289 - 0.361: 8 Chirality restraints: 3232 Sorted by residual: chirality pdb=" C2 POV D1101 " pdb=" C1 POV D1101 " pdb=" C3 POV D1101 " pdb=" O21 POV D1101 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C2 POV C1106 " pdb=" C1 POV C1106 " pdb=" C3 POV C1106 " pdb=" O21 POV C1106 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C2 POV A1105 " pdb=" C1 POV A1105 " pdb=" C3 POV A1105 " pdb=" O21 POV A1105 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 3229 not shown) Planarity restraints: 3604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO C 181 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 181 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO B 181 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.029 5.00e-02 4.00e+02 ... (remaining 3601 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 203 2.65 - 3.21: 17998 3.21 - 3.78: 32963 3.78 - 4.34: 49137 4.34 - 4.90: 77635 Nonbonded interactions: 177936 Sorted by model distance: nonbonded pdb="NA NA A1109 " pdb="NA NA A1110 " model vdw 2.088 1.900 nonbonded pdb="NA NA A1110 " pdb="NA NA A1111 " model vdw 2.114 1.900 nonbonded pdb=" O PRO B 753 " pdb=" OH TYR C 213 " model vdw 2.173 3.040 nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO D 753 " model vdw 2.218 3.040 ... (remaining 177931 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 1107) selection = (chain 'B' and resid 118 through 1107) selection = (chain 'C' and resid 118 through 1107) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.860 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 0.069 22392 Z= 0.288 Angle : 0.924 9.046 29968 Z= 0.466 Chirality : 0.053 0.361 3232 Planarity : 0.005 0.052 3604 Dihedral : 18.517 175.865 8992 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.36 % Allowed : 4.15 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (0.12), residues: 2484 helix: -3.95 (0.06), residues: 1640 sheet: 0.92 (0.50), residues: 112 loop : -2.27 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 690 TYR 0.028 0.003 TYR B 622 PHE 0.018 0.002 PHE C 316 TRP 0.020 0.002 TRP B 692 HIS 0.009 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.29 (22388) covalent geometry : angle 0.92375 / 0.47 (29960) SS BOND : bond 0.00370 / 0.19 ( 4) SS BOND : angle 1.14406 / 0.71 ( 8) hydrogen bonds : bond 0.30260 / 19.79 ( 1060) hydrogen bonds : angle 8.85019 / 6.16 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 515 time to evaluate : 0.784 Fit side-chains REVERT: A 488 MET cc_start: 0.6533 (mmp) cc_final: 0.6293 (mmm) REVERT: A 490 VAL cc_start: 0.7883 (m) cc_final: 0.7484 (t) REVERT: A 677 MET cc_start: 0.8228 (mtt) cc_final: 0.8015 (mtt) REVERT: A 698 ARG cc_start: 0.7853 (ttt90) cc_final: 0.7601 (ttt90) REVERT: A 704 GLU cc_start: 0.8361 (tt0) cc_final: 0.8011 (tt0) REVERT: B 488 MET cc_start: 0.6415 (mmp) cc_final: 0.6171 (mmt) REVERT: B 490 VAL cc_start: 0.7878 (m) cc_final: 0.7479 (t) REVERT: B 659 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 698 ARG cc_start: 0.7846 (ttt90) cc_final: 0.7557 (ttt90) REVERT: B 704 GLU cc_start: 0.8394 (tt0) cc_final: 0.8026 (tt0) REVERT: C 488 MET cc_start: 0.6510 (mmp) cc_final: 0.6270 (mmm) REVERT: C 490 VAL cc_start: 0.7908 (m) cc_final: 0.7471 (t) REVERT: C 649 LYS cc_start: 0.7238 (mtpt) cc_final: 0.6998 (mttt) REVERT: C 659 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8386 (mt) REVERT: C 704 GLU cc_start: 0.8399 (tt0) cc_final: 0.8062 (tt0) REVERT: D 401 ASN cc_start: 0.7013 (p0) cc_final: 0.6694 (p0) REVERT: D 488 MET cc_start: 0.6514 (mmp) cc_final: 0.6284 (mmm) REVERT: D 490 VAL cc_start: 0.7828 (m) cc_final: 0.7474 (t) REVERT: D 659 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8272 (mt) REVERT: D 677 MET cc_start: 0.8235 (mtt) cc_final: 0.8004 (mtt) REVERT: D 698 ARG cc_start: 0.7868 (ttt90) cc_final: 0.7625 (ttt90) REVERT: D 704 GLU cc_start: 0.8376 (tt0) cc_final: 0.8025 (tt0) outliers start: 8 outliers final: 4 residues processed: 523 average time/residue: 0.6798 time to fit residues: 399.5303 Evaluate side-chains 361 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 354 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 659 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 279 GLN A 410 ASN A 412 ASN A 452 ASN A 616 ASN A 695 GLN B 220 ASN B 410 ASN B 412 ASN B 616 ASN B 645 GLN B 695 GLN C 220 ASN C 279 GLN C 410 ASN C 412 ASN C 452 ASN C 580 GLN C 616 ASN C 645 GLN C 695 GLN D 410 ASN D 452 ASN D 616 ASN D 695 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.184137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.147878 restraints weight = 21727.188| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.23 r_work: 0.3341 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22392 Z= 0.116 Angle : 0.554 8.483 29968 Z= 0.290 Chirality : 0.040 0.191 3232 Planarity : 0.005 0.039 3604 Dihedral : 21.264 178.855 4106 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 11.24 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.16), residues: 2484 helix: -1.00 (0.12), residues: 1644 sheet: 1.00 (0.51), residues: 112 loop : -1.86 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 327 TYR 0.015 0.002 TYR C 321 PHE 0.011 0.001 PHE C 590 TRP 0.014 0.001 TRP D 692 HIS 0.008 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (22388) covalent geometry : angle 0.55409 / 0.29 (29960) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.60592 / 0.37 ( 8) hydrogen bonds : bond 0.04136 / 2.74 ( 1060) hydrogen bonds : angle 3.57299 / 2.46 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 361 time to evaluate : 0.805 Fit side-chains REVERT: A 233 LEU cc_start: 0.8264 (tt) cc_final: 0.7976 (tp) REVERT: A 257 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6697 (pm20) REVERT: A 401 ASN cc_start: 0.7619 (p0) cc_final: 0.7180 (p0) REVERT: A 488 MET cc_start: 0.7096 (mmp) cc_final: 0.6822 (mmm) REVERT: A 677 MET cc_start: 0.8325 (mtt) cc_final: 0.7838 (mtm) REVERT: A 687 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: B 257 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6682 (pm20) REVERT: B 401 ASN cc_start: 0.7625 (p0) cc_final: 0.7195 (p0) REVERT: B 488 MET cc_start: 0.7036 (mmp) cc_final: 0.6799 (mmm) REVERT: B 562 MET cc_start: 0.8772 (mmm) cc_final: 0.7736 (mmt) REVERT: B 677 MET cc_start: 0.8252 (mtt) cc_final: 0.7952 (mtm) REVERT: B 687 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: B 695 GLN cc_start: 0.8838 (mt0) cc_final: 0.8585 (mt0) REVERT: B 704 GLU cc_start: 0.8753 (tt0) cc_final: 0.8541 (tt0) REVERT: B 719 GLU cc_start: 0.8404 (pm20) cc_final: 0.7849 (pt0) REVERT: C 233 LEU cc_start: 0.8312 (tt) cc_final: 0.8050 (tp) REVERT: C 257 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6289 (mp0) REVERT: C 401 ASN cc_start: 0.7601 (p0) cc_final: 0.7141 (p0) REVERT: C 488 MET cc_start: 0.7107 (mmp) cc_final: 0.6856 (mmm) REVERT: C 580 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: C 649 LYS cc_start: 0.6994 (mtpt) cc_final: 0.6446 (mttt) REVERT: C 677 MET cc_start: 0.8207 (mtt) cc_final: 0.7888 (mtm) REVERT: C 687 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: D 257 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6656 (pm20) REVERT: D 401 ASN cc_start: 0.7620 (p0) cc_final: 0.7237 (p0) REVERT: D 488 MET cc_start: 0.7044 (mmp) cc_final: 0.6803 (mmm) REVERT: D 677 MET cc_start: 0.8350 (mtt) cc_final: 0.7865 (mtm) REVERT: D 687 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: D 695 GLN cc_start: 0.8839 (mt0) cc_final: 0.8616 (mt0) REVERT: D 704 GLU cc_start: 0.8729 (tt0) cc_final: 0.8527 (tt0) outliers start: 44 outliers final: 3 residues processed: 393 average time/residue: 0.7282 time to fit residues: 320.8720 Evaluate side-chains 329 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 321 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain D residue 687 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A 417 HIS B 279 GLN C 412 ASN C 417 HIS C 580 GLN D 279 GLN D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.177294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.140446 restraints weight = 20558.715| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.47 r_work: 0.3274 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22392 Z= 0.115 Angle : 0.518 7.998 29968 Z= 0.271 Chirality : 0.039 0.197 3232 Planarity : 0.004 0.037 3604 Dihedral : 20.270 159.084 4092 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.35 % Allowed : 12.05 % Favored : 85.60 % 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: -0.37 (0.17), residues: 2484 helix: 0.28 (0.13), residues: 1644 sheet: 1.26 (0.53), residues: 112 loop : -1.55 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.014 0.002 TYR B 594 PHE 0.020 0.001 PHE B 449 TRP 0.013 0.001 TRP C 692 HIS 0.007 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (22388) covalent geometry : angle 0.51752 / 0.27 (29960) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 0.85633 / 0.57 ( 8) hydrogen bonds : bond 0.04027 / 2.66 ( 1060) hydrogen bonds : angle 3.32783 / 2.29 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 325 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ASN cc_start: 0.7667 (p0) cc_final: 0.7259 (p0) REVERT: A 434 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8163 (tttt) REVERT: A 488 MET cc_start: 0.7121 (mmp) cc_final: 0.6898 (mmm) REVERT: A 677 MET cc_start: 0.8377 (mtt) cc_final: 0.7869 (mtm) REVERT: A 687 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: A 719 GLU cc_start: 0.8406 (pm20) cc_final: 0.7922 (pt0) REVERT: B 401 ASN cc_start: 0.7658 (p0) cc_final: 0.7227 (p0) REVERT: B 562 MET cc_start: 0.8734 (mmm) cc_final: 0.7855 (mmt) REVERT: B 687 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: B 719 GLU cc_start: 0.8454 (pm20) cc_final: 0.7965 (pt0) REVERT: B 734 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8954 (mp) REVERT: C 233 LEU cc_start: 0.8321 (tt) cc_final: 0.8044 (tp) REVERT: C 257 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6257 (mp0) REVERT: C 367 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: C 371 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7114 (tmm-80) REVERT: C 401 ASN cc_start: 0.7670 (p0) cc_final: 0.7249 (p0) REVERT: C 488 MET cc_start: 0.7148 (mmp) cc_final: 0.6930 (mmm) REVERT: C 580 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6752 (pp30) REVERT: C 649 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6403 (mttt) REVERT: C 677 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: C 687 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7332 (pp20) REVERT: C 719 GLU cc_start: 0.8451 (pm20) cc_final: 0.7952 (pt0) REVERT: C 734 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8942 (mp) REVERT: D 371 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7127 (tmm-80) REVERT: D 401 ASN cc_start: 0.7721 (p0) cc_final: 0.7410 (p0) REVERT: D 677 MET cc_start: 0.8381 (mtt) cc_final: 0.7863 (mtm) REVERT: D 687 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: D 719 GLU cc_start: 0.8410 (pm20) cc_final: 0.7940 (pt0) outliers start: 52 outliers final: 9 residues processed: 353 average time/residue: 0.6771 time to fit residues: 268.1936 Evaluate side-chains 335 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 687 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 ASN C 412 ASN C 580 GLN D 220 ASN D 417 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137804 restraints weight = 20579.132| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.44 r_work: 0.3234 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22392 Z= 0.138 Angle : 0.572 12.051 29968 Z= 0.292 Chirality : 0.041 0.220 3232 Planarity : 0.004 0.041 3604 Dihedral : 20.148 137.091 4092 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.81 % Allowed : 13.00 % Favored : 85.20 % 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: 0.18 (0.17), residues: 2484 helix: 0.70 (0.13), residues: 1644 sheet: 1.44 (0.54), residues: 112 loop : -1.32 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 327 TYR 0.016 0.002 TYR D 594 PHE 0.011 0.001 PHE C 590 TRP 0.013 0.001 TRP C 692 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22388) covalent geometry : angle 0.57125 / 0.29 (29960) SS BOND : bond 0.00356 / 0.18 ( 4) SS BOND : angle 1.32564 / 0.86 ( 8) hydrogen bonds : bond 0.04172 / 2.76 ( 1060) hydrogen bonds : angle 3.33415 / 2.29 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 ASN cc_start: 0.7839 (p0) cc_final: 0.7480 (p0) REVERT: A 534 ILE cc_start: 0.7796 (mm) cc_final: 0.7565 (mp) REVERT: A 572 MET cc_start: 0.8603 (mmm) cc_final: 0.8394 (mmm) REVERT: A 677 MET cc_start: 0.8432 (mtt) cc_final: 0.8186 (mtt) REVERT: A 719 GLU cc_start: 0.8442 (pm20) cc_final: 0.7974 (pt0) REVERT: A 734 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 401 ASN cc_start: 0.7834 (p0) cc_final: 0.7467 (p0) REVERT: B 562 MET cc_start: 0.8842 (mmm) cc_final: 0.7864 (mmt) REVERT: B 719 GLU cc_start: 0.8443 (pm20) cc_final: 0.7970 (pt0) REVERT: B 734 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8940 (mp) REVERT: C 257 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6434 (mp0) REVERT: C 371 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6925 (tmm-80) REVERT: C 401 ASN cc_start: 0.7818 (p0) cc_final: 0.7445 (p0) REVERT: C 580 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6972 (pp30) REVERT: C 649 LYS cc_start: 0.7110 (mtpt) cc_final: 0.6461 (mttt) REVERT: C 687 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7524 (pp20) REVERT: C 719 GLU cc_start: 0.8464 (pm20) cc_final: 0.7973 (pt0) REVERT: C 734 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8942 (mp) REVERT: D 257 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6419 (pm20) REVERT: D 371 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6998 (tmm-80) REVERT: D 401 ASN cc_start: 0.7777 (p0) cc_final: 0.7518 (p0) REVERT: D 677 MET cc_start: 0.8460 (mtt) cc_final: 0.8222 (mtt) REVERT: D 719 GLU cc_start: 0.8438 (pm20) cc_final: 0.7983 (pt0) REVERT: D 734 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8913 (mp) outliers start: 40 outliers final: 17 residues processed: 354 average time/residue: 0.7278 time to fit residues: 290.0361 Evaluate side-chains 343 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 318 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 62 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 417 HIS B 412 ASN B 417 HIS C 412 ASN C 417 HIS C 580 GLN D 417 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138752 restraints weight = 20595.569| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.44 r_work: 0.3251 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22392 Z= 0.119 Angle : 0.521 8.786 29968 Z= 0.271 Chirality : 0.039 0.217 3232 Planarity : 0.003 0.040 3604 Dihedral : 19.763 138.196 4092 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 12.64 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2484 helix: 0.99 (0.13), residues: 1648 sheet: 1.46 (0.54), residues: 112 loop : -1.17 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.014 0.002 TYR D 594 PHE 0.027 0.001 PHE C 449 TRP 0.011 0.001 TRP D 493 HIS 0.007 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (22388) covalent geometry : angle 0.51971 / 0.27 (29960) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 2.10466 / 1.38 ( 8) hydrogen bonds : bond 0.03767 / 2.49 ( 1060) hydrogen bonds : angle 3.27106 / 2.25 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 371 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7056 (ttm-80) REVERT: A 401 ASN cc_start: 0.7743 (p0) cc_final: 0.7343 (p0) REVERT: A 534 ILE cc_start: 0.7711 (mm) cc_final: 0.7472 (mp) REVERT: A 677 MET cc_start: 0.8410 (mtt) cc_final: 0.7860 (mtm) REVERT: A 687 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7147 (pp20) REVERT: A 719 GLU cc_start: 0.8408 (pm20) cc_final: 0.7944 (pt0) REVERT: A 734 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8935 (mp) REVERT: B 257 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6515 (pm20) REVERT: B 401 ASN cc_start: 0.7729 (p0) cc_final: 0.7325 (p0) REVERT: B 534 ILE cc_start: 0.7799 (mm) cc_final: 0.7553 (mp) REVERT: B 562 MET cc_start: 0.8770 (mmm) cc_final: 0.7840 (mmt) REVERT: B 677 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7892 (mtm) REVERT: B 687 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7159 (pp20) REVERT: B 719 GLU cc_start: 0.8427 (pm20) cc_final: 0.7962 (pt0) REVERT: C 257 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6489 (mp0) REVERT: C 371 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6996 (tmm-80) REVERT: C 401 ASN cc_start: 0.7736 (p0) cc_final: 0.7328 (p0) REVERT: C 649 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6474 (mttt) REVERT: C 687 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: C 719 GLU cc_start: 0.8430 (pm20) cc_final: 0.7953 (pt0) REVERT: D 257 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6446 (pm20) REVERT: D 371 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7001 (tmm-80) REVERT: D 401 ASN cc_start: 0.7690 (p0) cc_final: 0.7407 (p0) REVERT: D 534 ILE cc_start: 0.7821 (mm) cc_final: 0.7572 (mp) REVERT: D 677 MET cc_start: 0.8420 (mtt) cc_final: 0.7878 (mtm) REVERT: D 687 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7178 (pp20) REVERT: D 719 GLU cc_start: 0.8412 (pm20) cc_final: 0.7958 (pt0) REVERT: D 734 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8926 (mp) outliers start: 45 outliers final: 16 residues processed: 351 average time/residue: 0.7066 time to fit residues: 279.8165 Evaluate side-chains 348 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 322 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 204 optimal weight: 1.9990 chunk 170 optimal weight: 0.0870 chunk 124 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 ASN C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.173441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136215 restraints weight = 20763.702| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.49 r_work: 0.3227 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22392 Z= 0.134 Angle : 0.542 7.392 29968 Z= 0.284 Chirality : 0.040 0.234 3232 Planarity : 0.004 0.039 3604 Dihedral : 19.818 135.882 4092 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.03 % Allowed : 13.04 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.17), residues: 2484 helix: 1.12 (0.13), residues: 1644 sheet: 1.48 (0.54), residues: 112 loop : -1.10 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 327 TYR 0.016 0.002 TYR A 594 PHE 0.010 0.001 PHE A 449 TRP 0.014 0.002 TRP C 493 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (22388) covalent geometry : angle 0.54013 / 0.28 (29960) SS BOND : bond 0.00516 / 0.26 ( 4) SS BOND : angle 2.59811 / 1.70 ( 8) hydrogen bonds : bond 0.04092 / 2.71 ( 1060) hydrogen bonds : angle 3.31638 / 2.28 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6509 (pm20) REVERT: A 371 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7086 (tmm-80) REVERT: A 401 ASN cc_start: 0.7795 (p0) cc_final: 0.7429 (p0) REVERT: A 492 ILE cc_start: 0.7639 (mm) cc_final: 0.7288 (pt) REVERT: A 534 ILE cc_start: 0.7752 (mm) cc_final: 0.7512 (mp) REVERT: A 677 MET cc_start: 0.8431 (mtt) cc_final: 0.8198 (mtt) REVERT: A 719 GLU cc_start: 0.8431 (pm20) cc_final: 0.7994 (pt0) REVERT: A 734 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8920 (mp) REVERT: B 371 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7069 (tmm-80) REVERT: B 401 ASN cc_start: 0.7778 (p0) cc_final: 0.7416 (p0) REVERT: B 534 ILE cc_start: 0.7784 (mm) cc_final: 0.7524 (mp) REVERT: B 562 MET cc_start: 0.8796 (mmm) cc_final: 0.7851 (mmt) REVERT: B 719 GLU cc_start: 0.8445 (pm20) cc_final: 0.7997 (pt0) REVERT: B 734 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8898 (mp) REVERT: C 257 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6549 (mp0) REVERT: C 371 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6902 (tmm-80) REVERT: C 401 ASN cc_start: 0.7804 (p0) cc_final: 0.7432 (p0) REVERT: C 649 LYS cc_start: 0.7214 (mtpt) cc_final: 0.6528 (mttt) REVERT: C 687 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7479 (pp20) REVERT: C 719 GLU cc_start: 0.8437 (pm20) cc_final: 0.7953 (pt0) REVERT: C 734 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8908 (mp) REVERT: D 371 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6912 (tmm-80) REVERT: D 401 ASN cc_start: 0.7705 (p0) cc_final: 0.7447 (p0) REVERT: D 534 ILE cc_start: 0.7800 (mm) cc_final: 0.7538 (mp) REVERT: D 677 MET cc_start: 0.8455 (mtt) cc_final: 0.8230 (mtt) REVERT: D 719 GLU cc_start: 0.8436 (pm20) cc_final: 0.7992 (pt0) REVERT: D 734 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8911 (mp) outliers start: 45 outliers final: 26 residues processed: 357 average time/residue: 0.6386 time to fit residues: 258.3520 Evaluate side-chains 360 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 30 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 279 GLN B 412 ASN C 279 GLN C 412 ASN D 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142856 restraints weight = 21738.202| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.25 r_work: 0.3330 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22392 Z= 0.114 Angle : 0.503 6.544 29968 Z= 0.264 Chirality : 0.039 0.217 3232 Planarity : 0.003 0.039 3604 Dihedral : 19.457 136.992 4092 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.81 % Allowed : 13.31 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2484 helix: 1.29 (0.13), residues: 1648 sheet: 1.44 (0.54), residues: 112 loop : -1.11 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 327 TYR 0.013 0.002 TYR D 594 PHE 0.025 0.001 PHE C 449 TRP 0.014 0.001 TRP D 493 HIS 0.007 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (22388) covalent geometry : angle 0.50115 / 0.26 (29960) SS BOND : bond 0.00394 / 0.20 ( 4) SS BOND : angle 2.57394 / 1.67 ( 8) hydrogen bonds : bond 0.03621 / 2.40 ( 1060) hydrogen bonds : angle 3.22197 / 2.22 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 0.777 Fit side-chains REVERT: A 257 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6658 (pm20) REVERT: A 371 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7058 (ttm-80) REVERT: A 401 ASN cc_start: 0.7420 (p0) cc_final: 0.7042 (p0) REVERT: A 488 MET cc_start: 0.7065 (mmp) cc_final: 0.6784 (mmm) REVERT: A 534 ILE cc_start: 0.7898 (mm) cc_final: 0.7660 (mp) REVERT: A 677 MET cc_start: 0.8522 (mtt) cc_final: 0.8306 (mtt) REVERT: A 687 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: A 719 GLU cc_start: 0.8312 (pm20) cc_final: 0.7878 (pt0) REVERT: A 734 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8889 (mp) REVERT: B 257 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6777 (pm20) REVERT: B 371 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7093 (ttm-80) REVERT: B 401 ASN cc_start: 0.7405 (p0) cc_final: 0.7041 (p0) REVERT: B 534 ILE cc_start: 0.7975 (mm) cc_final: 0.7716 (mp) REVERT: B 562 MET cc_start: 0.8708 (mmm) cc_final: 0.7800 (mmt) REVERT: B 687 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: B 719 GLU cc_start: 0.8325 (pm20) cc_final: 0.7902 (pt0) REVERT: B 734 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8872 (mp) REVERT: C 257 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6827 (mp0) REVERT: C 371 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7079 (tmm-80) REVERT: C 401 ASN cc_start: 0.7434 (p0) cc_final: 0.7065 (p0) REVERT: C 649 LYS cc_start: 0.7180 (mtpt) cc_final: 0.6625 (mttt) REVERT: C 677 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: C 687 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: C 719 GLU cc_start: 0.8302 (pm20) cc_final: 0.7834 (pt0) REVERT: C 734 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8909 (mp) REVERT: D 257 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6721 (pm20) REVERT: D 371 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7042 (tmm-80) REVERT: D 401 ASN cc_start: 0.7331 (p0) cc_final: 0.7099 (p0) REVERT: D 534 ILE cc_start: 0.7974 (mm) cc_final: 0.7714 (mp) REVERT: D 677 MET cc_start: 0.8530 (mtt) cc_final: 0.8320 (mtt) REVERT: D 687 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7243 (pp20) REVERT: D 719 GLU cc_start: 0.8312 (pm20) cc_final: 0.7870 (pt0) REVERT: D 734 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8879 (mp) outliers start: 40 outliers final: 16 residues processed: 358 average time/residue: 0.6887 time to fit residues: 278.6295 Evaluate side-chains 360 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 750 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 197 optimal weight: 0.4980 chunk 198 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 412 ASN C 412 ASN D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.180676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144821 restraints weight = 21930.133| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.35 r_work: 0.3347 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22392 Z= 0.094 Angle : 0.467 5.605 29968 Z= 0.246 Chirality : 0.037 0.195 3232 Planarity : 0.003 0.039 3604 Dihedral : 18.977 136.015 4092 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.49 % Allowed : 13.99 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2484 helix: 1.47 (0.13), residues: 1652 sheet: 1.48 (0.53), residues: 112 loop : -1.09 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 327 TYR 0.011 0.001 TYR C 359 PHE 0.013 0.001 PHE A 316 TRP 0.016 0.001 TRP C 493 HIS 0.007 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (22388) covalent geometry : angle 0.46493 / 0.25 (29960) SS BOND : bond 0.00512 / 0.26 ( 4) SS BOND : angle 2.42017 / 1.57 ( 8) hydrogen bonds : bond 0.03161 / 2.10 ( 1060) hydrogen bonds : angle 3.15552 / 2.17 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 0.825 Fit side-chains REVERT: A 257 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6745 (pm20) REVERT: A 371 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7047 (ttm-80) REVERT: A 401 ASN cc_start: 0.7307 (p0) cc_final: 0.6899 (p0) REVERT: A 488 MET cc_start: 0.7119 (mmp) cc_final: 0.6840 (mmm) REVERT: A 534 ILE cc_start: 0.7898 (mm) cc_final: 0.7660 (mp) REVERT: A 618 ASP cc_start: 0.7359 (m-30) cc_final: 0.6832 (t0) REVERT: A 677 MET cc_start: 0.8516 (mtt) cc_final: 0.8017 (mtm) REVERT: A 687 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: A 719 GLU cc_start: 0.8299 (pm20) cc_final: 0.7876 (pt0) REVERT: A 734 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8915 (mp) REVERT: B 233 LEU cc_start: 0.8349 (tt) cc_final: 0.8073 (tp) REVERT: B 257 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6808 (pm20) REVERT: B 371 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7042 (ttm-80) REVERT: B 401 ASN cc_start: 0.7294 (p0) cc_final: 0.6892 (p0) REVERT: B 534 ILE cc_start: 0.7986 (mm) cc_final: 0.7729 (mp) REVERT: B 562 MET cc_start: 0.8642 (mmm) cc_final: 0.7886 (mmt) REVERT: B 618 ASP cc_start: 0.7334 (m-30) cc_final: 0.6830 (t0) REVERT: B 677 MET cc_start: 0.8448 (mtt) cc_final: 0.8046 (mtm) REVERT: B 687 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7262 (pp20) REVERT: B 719 GLU cc_start: 0.8373 (pm20) cc_final: 0.7947 (pt0) REVERT: B 734 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8904 (mp) REVERT: C 233 LEU cc_start: 0.8308 (tt) cc_final: 0.8054 (tp) REVERT: C 257 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6753 (pm20) REVERT: C 371 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7120 (tmm-80) REVERT: C 401 ASN cc_start: 0.7300 (p0) cc_final: 0.6880 (p0) REVERT: C 488 MET cc_start: 0.7042 (mmp) cc_final: 0.6765 (mmm) REVERT: C 535 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8051 (mt) REVERT: C 618 ASP cc_start: 0.7358 (m-30) cc_final: 0.6838 (t0) REVERT: C 649 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6592 (mttt) REVERT: C 677 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8118 (mtm) REVERT: C 687 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: C 719 GLU cc_start: 0.8298 (pm20) cc_final: 0.7826 (pt0) REVERT: C 734 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8906 (mp) REVERT: D 233 LEU cc_start: 0.8321 (tt) cc_final: 0.8060 (tp) REVERT: D 257 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6797 (pm20) REVERT: D 371 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7122 (tmm-80) REVERT: D 401 ASN cc_start: 0.7270 (p0) cc_final: 0.7002 (p0) REVERT: D 534 ILE cc_start: 0.7986 (mm) cc_final: 0.7724 (mp) REVERT: D 618 ASP cc_start: 0.7298 (m-30) cc_final: 0.6811 (t0) REVERT: D 677 MET cc_start: 0.8544 (mtt) cc_final: 0.8043 (mtm) REVERT: D 687 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7273 (pp20) REVERT: D 719 GLU cc_start: 0.8298 (pm20) cc_final: 0.7841 (pt0) REVERT: D 734 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8905 (mp) outliers start: 33 outliers final: 13 residues processed: 366 average time/residue: 0.6272 time to fit residues: 261.1509 Evaluate side-chains 353 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 326 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 37 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 412 ASN B 330 ASN B 412 ASN C 330 ASN C 412 ASN D 330 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143530 restraints weight = 21764.256| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.17 r_work: 0.3361 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22392 Z= 0.140 Angle : 0.540 5.977 29968 Z= 0.283 Chirality : 0.041 0.235 3232 Planarity : 0.003 0.040 3604 Dihedral : 19.443 134.282 4092 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.85 % Allowed : 13.72 % Favored : 84.43 % 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: 0.99 (0.17), residues: 2484 helix: 1.34 (0.13), residues: 1648 sheet: 1.52 (0.53), residues: 112 loop : -1.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.016 0.002 TYR C 594 PHE 0.021 0.001 PHE C 449 TRP 0.022 0.002 TRP C 493 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (22388) covalent geometry : angle 0.53821 / 0.28 (29960) SS BOND : bond 0.00533 / 0.27 ( 4) SS BOND : angle 2.51046 / 1.62 ( 8) hydrogen bonds : bond 0.04089 / 2.70 ( 1060) hydrogen bonds : angle 3.29617 / 2.26 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 331 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7175 (tmm-80) REVERT: A 401 ASN cc_start: 0.7727 (p0) cc_final: 0.7379 (p0) REVERT: A 488 MET cc_start: 0.7228 (mmp) cc_final: 0.6875 (mmt) REVERT: A 677 MET cc_start: 0.8575 (mtt) cc_final: 0.8320 (mtt) REVERT: A 719 GLU cc_start: 0.8381 (pm20) cc_final: 0.7958 (pt0) REVERT: A 734 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8899 (mp) REVERT: B 371 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7155 (tmm-80) REVERT: B 401 ASN cc_start: 0.7714 (p0) cc_final: 0.7377 (p0) REVERT: B 534 ILE cc_start: 0.7930 (mm) cc_final: 0.7663 (mp) REVERT: B 562 MET cc_start: 0.8758 (mmm) cc_final: 0.7874 (mmt) REVERT: B 719 GLU cc_start: 0.8448 (pm20) cc_final: 0.7996 (pt0) REVERT: B 734 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8876 (mp) REVERT: C 257 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6837 (mp0) REVERT: C 309 ASP cc_start: 0.8717 (p0) cc_final: 0.8412 (p0) REVERT: C 371 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7029 (tmm-80) REVERT: C 401 ASN cc_start: 0.7733 (p0) cc_final: 0.7396 (p0) REVERT: C 488 MET cc_start: 0.7188 (mmp) cc_final: 0.6845 (mmt) REVERT: C 618 ASP cc_start: 0.7443 (m-30) cc_final: 0.6802 (t0) REVERT: C 649 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6670 (mttt) REVERT: C 677 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8068 (mtm) REVERT: C 687 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: C 719 GLU cc_start: 0.8341 (pm20) cc_final: 0.7931 (pt0) REVERT: C 734 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8916 (mp) REVERT: D 371 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6995 (tmm-80) REVERT: D 401 ASN cc_start: 0.7558 (p0) cc_final: 0.7339 (p0) REVERT: D 534 ILE cc_start: 0.7937 (mm) cc_final: 0.7665 (mp) REVERT: D 618 ASP cc_start: 0.7462 (m-30) cc_final: 0.6847 (t0) REVERT: D 677 MET cc_start: 0.8570 (mtt) cc_final: 0.8314 (mtt) REVERT: D 719 GLU cc_start: 0.8375 (pm20) cc_final: 0.7942 (pt0) REVERT: D 734 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8889 (mp) outliers start: 41 outliers final: 21 residues processed: 354 average time/residue: 0.6834 time to fit residues: 274.0091 Evaluate side-chains 359 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 77 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 412 ASN B 330 ASN B 412 ASN C 330 ASN C 412 ASN D 330 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.176873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143172 restraints weight = 21892.673| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.15 r_work: 0.3376 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22392 Z= 0.172 Angle : 1.033 59.200 29968 Z= 0.606 Chirality : 0.040 0.229 3232 Planarity : 0.004 0.040 3604 Dihedral : 19.433 134.306 4092 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.31 % Allowed : 14.21 % Favored : 84.48 % 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: 0.99 (0.17), residues: 2484 helix: 1.35 (0.13), residues: 1648 sheet: 1.50 (0.53), residues: 112 loop : -1.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 122 TYR 0.015 0.002 TYR C 594 PHE 0.020 0.001 PHE C 449 TRP 0.019 0.002 TRP C 493 HIS 0.007 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (22388) covalent geometry : angle 1.03215 / 0.61 (29960) SS BOND : bond 0.00934 / 0.47 ( 4) SS BOND : angle 2.89117 / 1.90 ( 8) hydrogen bonds : bond 0.03973 / 2.63 ( 1060) hydrogen bonds : angle 3.29408 / 2.26 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7160 (tmm-80) REVERT: A 401 ASN cc_start: 0.7700 (p0) cc_final: 0.7357 (p0) REVERT: A 488 MET cc_start: 0.7214 (mmp) cc_final: 0.6863 (mmt) REVERT: A 677 MET cc_start: 0.8553 (mtt) cc_final: 0.8305 (mtt) REVERT: A 719 GLU cc_start: 0.8385 (pm20) cc_final: 0.7952 (pt0) REVERT: A 734 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8889 (mp) REVERT: B 371 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7154 (tmm-80) REVERT: B 401 ASN cc_start: 0.7693 (p0) cc_final: 0.7359 (p0) REVERT: B 534 ILE cc_start: 0.7925 (mm) cc_final: 0.7657 (mp) REVERT: B 562 MET cc_start: 0.8746 (mmm) cc_final: 0.7865 (mmt) REVERT: B 687 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: B 719 GLU cc_start: 0.8445 (pm20) cc_final: 0.7997 (pt0) REVERT: B 734 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8869 (mp) REVERT: C 257 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6833 (mp0) REVERT: C 309 ASP cc_start: 0.8713 (p0) cc_final: 0.8407 (p0) REVERT: C 371 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7012 (tmm-80) REVERT: C 401 ASN cc_start: 0.7710 (p0) cc_final: 0.7373 (p0) REVERT: C 488 MET cc_start: 0.7164 (mmp) cc_final: 0.6824 (mmt) REVERT: C 618 ASP cc_start: 0.7435 (m-30) cc_final: 0.6802 (t0) REVERT: C 649 LYS cc_start: 0.7260 (mtpt) cc_final: 0.6650 (mttt) REVERT: C 677 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8054 (mtm) REVERT: C 687 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7525 (pp20) REVERT: C 719 GLU cc_start: 0.8368 (pm20) cc_final: 0.7934 (pt0) REVERT: C 734 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8906 (mp) REVERT: D 371 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6979 (tmm-80) REVERT: D 401 ASN cc_start: 0.7537 (p0) cc_final: 0.7318 (p0) REVERT: D 618 ASP cc_start: 0.7452 (m-30) cc_final: 0.6843 (t0) REVERT: D 677 MET cc_start: 0.8568 (mtt) cc_final: 0.8313 (mtt) REVERT: D 687 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: D 719 GLU cc_start: 0.8362 (pm20) cc_final: 0.7918 (pt0) REVERT: D 734 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8877 (mp) outliers start: 29 outliers final: 14 residues processed: 346 average time/residue: 0.6952 time to fit residues: 272.7314 Evaluate side-chains 354 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 328 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 107 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 63 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.1980 chunk 133 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 412 ASN C 412 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.176863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142485 restraints weight = 21767.073| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.21 r_work: 0.3367 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22392 Z= 0.173 Angle : 1.034 59.200 29968 Z= 0.606 Chirality : 0.040 0.229 3232 Planarity : 0.004 0.040 3604 Dihedral : 19.433 134.306 4092 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.17 % Allowed : 14.35 % Favored : 84.48 % 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: 0.99 (0.17), residues: 2484 helix: 1.35 (0.13), residues: 1648 sheet: 1.50 (0.53), residues: 112 loop : -1.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 122 TYR 0.015 0.002 TYR C 594 PHE 0.020 0.001 PHE C 449 TRP 0.019 0.002 TRP C 493 HIS 0.007 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (22388) covalent geometry : angle 1.03215 / 0.61 (29960) SS BOND : bond 0.03675 / 1.84 ( 4) SS BOND : angle 3.49142 / 2.38 ( 8) hydrogen bonds : bond 0.03973 / 2.63 ( 1060) hydrogen bonds : angle 3.29408 / 2.26 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10364.69 seconds wall clock time: 176 minutes 32.41 seconds (10592.41 seconds total)