Starting phenix.real_space_refine on Fri Aug 7 17:00:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pj5_71680/08_2026/9pj5_71680.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pj5_71680/08_2026/9pj5_71680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pj5_71680/08_2026/9pj5_71680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pj5_71680/08_2026/9pj5_71680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pj5_71680/08_2026/9pj5_71680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pj5_71680/08_2026/9pj5_71680.map" } resolution = 2.76 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= 0.001 sd= 0.031 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 2 4.78 5 C 14552 2.51 5 N 3388 2.21 5 O 4180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 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: 22278 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5075 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5075 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "C" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5075 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "D" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5075 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 15, 'TRANS': 607} Chain breaks: 1 Chain: "A" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 418 Unusual residues: {' NA': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" 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: "C" 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: "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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Time building chain proxies: 5.04, per 1000 atoms: 0.23 Number of scatterers: 22278 At special positions: 0 Unit cell: (161.33, 161.33, 128.48, 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 2 11.00 O 4180 8.00 N 3388 7.00 C 14552 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=2.03 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 790.6 milliseconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4768 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 65.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.730A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 removed outlier: 3.707A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.737A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.563A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.701A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.572A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.526A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.585A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.770A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.609A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.511A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) 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 removed outlier: 3.523A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.589A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 482 through 507 removed outlier: 3.771A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.527A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.905A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.547A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.556A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.591A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.652A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.582A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 4.128A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.730A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.706A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.738A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 159' Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.563A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.701A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.572A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.526A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.585A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.768A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.609A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.513A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) 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 removed outlier: 3.523A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.589A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 482 through 507 removed outlier: 3.770A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.525A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.905A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.547A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.557A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.591A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.652A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.583A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 4.129A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.730A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.706A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.738A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.562A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.701A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.571A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.526A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.585A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 331 through 336 removed outlier: 3.770A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.609A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.512A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) 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 removed outlier: 3.523A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.590A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 482 through 507 removed outlier: 3.770A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.526A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.906A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.547A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.558A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.591A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.653A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.583A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 4.129A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.731A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 147 removed outlier: 3.706A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.738A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 159' Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.563A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.702A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.572A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.525A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.585A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.769A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.609A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.513A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) 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 removed outlier: 3.523A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.587A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 482 through 507 removed outlier: 3.771A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.527A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.904A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.547A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.557A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.592A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.653A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.583A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 4.129A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.790A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.106A 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: 6.791A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.106A 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: 6.790A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.105A 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: 6.791A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2964 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: 3.18 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3324 1.31 - 1.44: 5856 1.44 - 1.56: 12928 1.56 - 1.69: 64 1.69 - 1.81: 204 Bond restraints: 22376 Sorted by residual: bond pdb=" C21 POV C 905 " pdb=" O21 POV C 905 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C21 POV A 906 " pdb=" O21 POV A 906 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV B 905 " pdb=" O21 POV B 905 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C21 POV C 909 " pdb=" O21 POV C 909 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C21 POV A 908 " pdb=" O21 POV A 908 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 22371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 28748 2.58 - 5.16: 770 5.16 - 7.74: 243 7.74 - 10.32: 119 10.32 - 12.90: 72 Bond angle restraints: 29952 Sorted by residual: angle pdb=" C ASP B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 120.33 124.80 -4.47 8.00e-01 1.56e+00 3.12e+01 angle pdb=" C ASP A 153 " pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.07e+01 angle pdb=" C ASP D 153 " pdb=" N VAL D 154 " pdb=" CA VAL D 154 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.02e+01 angle pdb=" C ASP C 153 " pdb=" N VAL C 154 " pdb=" CA VAL C 154 " ideal model delta sigma weight residual 120.33 124.70 -4.37 8.00e-01 1.56e+00 2.98e+01 angle pdb=" C LYS C 368 " pdb=" N ARG C 369 " pdb=" CA ARG C 369 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 ... (remaining 29947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 13119 35.81 - 71.61: 546 71.61 - 107.42: 41 107.42 - 143.22: 34 143.22 - 179.03: 16 Dihedral angle restraints: 13756 sinusoidal: 6412 harmonic: 7344 Sorted by residual: dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N GLU A 423 " pdb=" CA GLU A 423 " ideal model delta harmonic sigma weight residual -180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LEU B 422 " pdb=" C LEU B 422 " pdb=" N GLU B 423 " pdb=" CA GLU B 423 " ideal model delta harmonic sigma weight residual 180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU D 422 " pdb=" C LEU D 422 " pdb=" N GLU D 423 " pdb=" CA GLU D 423 " ideal model delta harmonic sigma weight residual -180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 13753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2681 0.059 - 0.118: 493 0.118 - 0.177: 42 0.177 - 0.236: 6 0.236 - 0.295: 6 Chirality restraints: 3228 Sorted by residual: chirality pdb=" CG LEU B 135 " pdb=" CB LEU B 135 " pdb=" CD1 LEU B 135 " pdb=" CD2 LEU B 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CG LEU A 135 " pdb=" CB LEU A 135 " pdb=" CD1 LEU A 135 " pdb=" CD2 LEU A 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU C 135 " pdb=" CB LEU C 135 " pdb=" CD1 LEU C 135 " pdb=" CD2 LEU C 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 3225 not shown) Planarity restraints: 3596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.046 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO B 181 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO C 181 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 181 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.039 5.00e-02 4.00e+02 ... (remaining 3593 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6653 2.83 - 3.35: 18947 3.35 - 3.86: 36416 3.86 - 4.38: 45377 4.38 - 4.90: 75268 Nonbonded interactions: 182661 Sorted by model distance: nonbonded pdb=" O HOH C1022 " pdb=" O HOH C1055 " model vdw 2.310 3.040 nonbonded pdb=" O PRO B 753 " pdb=" OH TYR C 213 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLU D 355 " pdb=" O HOH D1001 " model vdw 2.318 3.040 nonbonded pdb=" OE1 GLU A 355 " pdb=" O HOH A1001 " model vdw 2.327 3.040 nonbonded pdb=" O HOH D1047 " pdb=" O HOH D1075 " model vdw 2.332 3.040 ... (remaining 182656 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 907) selection = (chain 'B' and resid 118 through 907) selection = (chain 'C' and resid 118 through 907) 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.720 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.010 0.097 22388 Z= 0.478 Angle : 1.343 12.899 29960 Z= 0.618 Chirality : 0.047 0.295 3228 Planarity : 0.005 0.071 3596 Dihedral : 19.730 179.031 8976 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % 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: -5.53 (0.12), residues: 2476 helix: -4.42 (0.05), residues: 1564 sheet: 0.09 (0.51), residues: 112 loop : -2.00 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 462 TYR 0.028 0.003 TYR D 622 PHE 0.041 0.002 PHE D 526 TRP 0.018 0.002 TRP A 692 HIS 0.009 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00962 / 0.48 (22376) covalent geometry : angle 1.34271 / 0.62 (29952) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 0.49352 / 0.35 ( 8) hydrogen bonds : bond 0.32862 / 21.75 ( 1008) hydrogen bonds : angle 9.79257 / 6.81 ( 2964) Misc. bond : bond 0.00247 / 0.14 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 401 time to evaluate : 0.654 Fit side-chains REVERT: A 276 GLU cc_start: 0.7362 (mp0) cc_final: 0.7112 (mp0) REVERT: A 280 LEU cc_start: 0.8164 (tp) cc_final: 0.7939 (tp) REVERT: A 493 TRP cc_start: 0.7124 (t-100) cc_final: 0.6807 (t-100) REVERT: A 495 MET cc_start: 0.7112 (mmm) cc_final: 0.6745 (mmt) REVERT: A 514 GLN cc_start: 0.6708 (pt0) cc_final: 0.6377 (mp10) REVERT: A 627 ASP cc_start: 0.7634 (m-30) cc_final: 0.7259 (m-30) REVERT: A 698 ARG cc_start: 0.7432 (ttt90) cc_final: 0.7089 (mtt90) REVERT: A 716 ARG cc_start: 0.7417 (ttp80) cc_final: 0.6549 (tpm170) REVERT: A 751 GLU cc_start: 0.7096 (pt0) cc_final: 0.6864 (pt0) REVERT: B 280 LEU cc_start: 0.8121 (tp) cc_final: 0.7874 (tp) REVERT: B 495 MET cc_start: 0.7026 (mmm) cc_final: 0.6628 (mmt) REVERT: B 514 GLN cc_start: 0.6659 (pt0) cc_final: 0.6367 (mp10) REVERT: B 627 ASP cc_start: 0.7654 (m-30) cc_final: 0.7298 (m-30) REVERT: B 698 ARG cc_start: 0.7371 (ttt90) cc_final: 0.7051 (mtt90) REVERT: B 716 ARG cc_start: 0.7470 (ttp80) cc_final: 0.6667 (tpm170) REVERT: B 751 GLU cc_start: 0.7225 (pt0) cc_final: 0.6838 (pt0) REVERT: C 129 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6043 (mm-30) REVERT: C 493 TRP cc_start: 0.7118 (t-100) cc_final: 0.6820 (t-100) REVERT: C 495 MET cc_start: 0.7121 (mmm) cc_final: 0.6824 (mmt) REVERT: C 514 GLN cc_start: 0.6697 (pt0) cc_final: 0.6406 (mp10) REVERT: C 627 ASP cc_start: 0.7657 (m-30) cc_final: 0.7306 (m-30) REVERT: C 698 ARG cc_start: 0.7526 (ttt90) cc_final: 0.7168 (mtt90) REVERT: C 716 ARG cc_start: 0.7583 (ttp80) cc_final: 0.6682 (tpm170) REVERT: C 751 GLU cc_start: 0.7547 (pt0) cc_final: 0.7179 (pt0) REVERT: D 276 GLU cc_start: 0.7250 (mp0) cc_final: 0.6931 (mp0) REVERT: D 280 LEU cc_start: 0.7954 (tp) cc_final: 0.7669 (tp) REVERT: D 332 GLU cc_start: 0.7010 (tt0) cc_final: 0.6538 (tp30) REVERT: D 338 ASN cc_start: 0.7619 (p0) cc_final: 0.7251 (p0) REVERT: D 488 MET cc_start: 0.6233 (mmp) cc_final: 0.5783 (tpp) REVERT: D 493 TRP cc_start: 0.6969 (t-100) cc_final: 0.6589 (t-100) REVERT: D 495 MET cc_start: 0.7023 (mmm) cc_final: 0.6670 (mmt) REVERT: D 514 GLN cc_start: 0.6536 (pt0) cc_final: 0.6143 (mp10) REVERT: D 627 ASP cc_start: 0.7617 (m-30) cc_final: 0.7233 (m-30) REVERT: D 698 ARG cc_start: 0.7284 (ttt90) cc_final: 0.6845 (mtt90) REVERT: D 716 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6372 (tpm170) outliers start: 4 outliers final: 0 residues processed: 401 average time/residue: 0.6291 time to fit residues: 284.4873 Evaluate side-chains 251 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 220 ASN A 227 GLN A 314 ASN A 401 ASN A 412 ASN A 417 HIS B 178 ASN B 220 ASN B 227 GLN B 314 ASN B 401 ASN B 412 ASN B 417 HIS C 178 ASN C 314 ASN C 401 ASN C 412 ASN C 417 HIS D 178 ASN D 220 ASN D 227 GLN D 314 ASN D 401 ASN D 412 ASN D 417 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.173184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.125098 restraints weight = 22661.055| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.78 r_work: 0.3057 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22388 Z= 0.129 Angle : 0.588 6.980 29960 Z= 0.299 Chirality : 0.038 0.206 3228 Planarity : 0.005 0.050 3596 Dihedral : 23.660 178.048 4084 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.44 % Allowed : 5.61 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.15), residues: 2476 helix: -1.76 (0.11), residues: 1596 sheet: 0.23 (0.50), residues: 112 loop : -1.68 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 327 TYR 0.012 0.002 TYR C 208 PHE 0.012 0.001 PHE D 526 TRP 0.013 0.001 TRP C 692 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22376) covalent geometry : angle 0.58774 / 0.30 (29952) SS BOND : bond 0.00023 / 0.01 ( 4) SS BOND : angle 0.30269 / 0.22 ( 8) hydrogen bonds : bond 0.05328 / 3.50 ( 1008) hydrogen bonds : angle 3.99100 / 2.72 ( 2964) Misc. bond : bond 0.00059 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.681 Fit side-chains REVERT: A 276 GLU cc_start: 0.7790 (mp0) cc_final: 0.7487 (mp0) REVERT: A 434 LYS cc_start: 0.8183 (mtpm) cc_final: 0.7825 (mptt) REVERT: A 488 MET cc_start: 0.7021 (tpp) cc_final: 0.6067 (tpp) REVERT: A 493 TRP cc_start: 0.7565 (t-100) cc_final: 0.7080 (t-100) REVERT: A 514 GLN cc_start: 0.6971 (pt0) cc_final: 0.6335 (mp10) REVERT: A 635 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8179 (mt) REVERT: A 698 ARG cc_start: 0.8411 (ttt90) cc_final: 0.7493 (mtm-85) REVERT: A 706 MET cc_start: 0.7917 (mtt) cc_final: 0.7708 (mtp) REVERT: A 713 SER cc_start: 0.7808 (m) cc_final: 0.7472 (p) REVERT: A 714 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7326 (mmm160) REVERT: A 716 ARG cc_start: 0.7768 (ttp80) cc_final: 0.6469 (tpm170) REVERT: A 751 GLU cc_start: 0.7924 (pt0) cc_final: 0.7476 (pt0) REVERT: B 229 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: B 514 GLN cc_start: 0.6958 (pt0) cc_final: 0.6324 (mp10) REVERT: B 698 ARG cc_start: 0.8424 (ttt90) cc_final: 0.7552 (mtm-85) REVERT: B 714 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7240 (mmm160) REVERT: B 716 ARG cc_start: 0.7759 (ttp80) cc_final: 0.6409 (tpm170) REVERT: B 751 GLU cc_start: 0.7965 (pt0) cc_final: 0.7521 (pt0) REVERT: C 327 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7189 (tmt-80) REVERT: C 488 MET cc_start: 0.7001 (tpp) cc_final: 0.6625 (tpt) REVERT: C 514 GLN cc_start: 0.7017 (pt0) cc_final: 0.6344 (mp10) REVERT: C 698 ARG cc_start: 0.8499 (ttt90) cc_final: 0.7551 (mtm-85) REVERT: C 713 SER cc_start: 0.7820 (m) cc_final: 0.7518 (p) REVERT: C 714 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7381 (mmm160) REVERT: C 716 ARG cc_start: 0.7879 (ttp80) cc_final: 0.6584 (tpm170) REVERT: D 229 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: D 276 GLU cc_start: 0.7758 (mp0) cc_final: 0.7403 (mp0) REVERT: D 332 GLU cc_start: 0.8057 (tt0) cc_final: 0.7306 (tp30) REVERT: D 434 LYS cc_start: 0.8178 (mtpm) cc_final: 0.7812 (mptt) REVERT: D 493 TRP cc_start: 0.7552 (t-100) cc_final: 0.7047 (t-100) REVERT: D 514 GLN cc_start: 0.6932 (pt0) cc_final: 0.6322 (mp10) REVERT: D 698 ARG cc_start: 0.8417 (ttt90) cc_final: 0.7515 (mtm-85) REVERT: D 713 SER cc_start: 0.7849 (m) cc_final: 0.7526 (p) REVERT: D 716 ARG cc_start: 0.7706 (ttp80) cc_final: 0.6424 (tpm170) outliers start: 54 outliers final: 5 residues processed: 335 average time/residue: 0.5965 time to fit residues: 228.7679 Evaluate side-chains 276 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 108 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN A 426 HIS B 412 ASN B 426 HIS C 412 ASN C 426 HIS D 412 ASN D 426 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.160196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107686 restraints weight = 22126.449| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.87 r_work: 0.2861 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22388 Z= 0.277 Angle : 0.730 9.311 29960 Z= 0.357 Chirality : 0.046 0.209 3228 Planarity : 0.005 0.051 3596 Dihedral : 23.078 157.832 4084 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.15 % Favored : 96.53 % Rotamer: Outliers : 2.94 % Allowed : 7.87 % Favored : 89.20 % 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: -1.16 (0.16), residues: 2476 helix: -0.47 (0.12), residues: 1584 sheet: 0.33 (0.50), residues: 112 loop : -1.27 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 696 TYR 0.029 0.003 TYR D 359 PHE 0.021 0.003 PHE A 449 TRP 0.019 0.002 TRP C 692 HIS 0.011 0.002 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.28 (22376) covalent geometry : angle 0.73011 / 0.36 (29952) SS BOND : bond 0.00028 / 0.01 ( 4) SS BOND : angle 0.53514 / 0.38 ( 8) hydrogen bonds : bond 0.05966 / 3.94 ( 1008) hydrogen bonds : angle 4.11451 / 2.83 ( 2964) Misc. bond : bond 0.00123 / 0.08 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.682 Fit side-chains REVERT: A 184 LYS cc_start: 0.6969 (ttmt) cc_final: 0.6649 (tttm) REVERT: A 233 LEU cc_start: 0.7619 (tt) cc_final: 0.7378 (tp) REVERT: A 276 GLU cc_start: 0.7799 (mp0) cc_final: 0.7461 (mp0) REVERT: A 279 GLN cc_start: 0.8045 (mt0) cc_final: 0.7737 (mt0) REVERT: A 280 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 286 GLN cc_start: 0.8363 (mt0) cc_final: 0.8062 (mm110) REVERT: A 431 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7592 (mpm) REVERT: A 434 LYS cc_start: 0.8288 (mtpm) cc_final: 0.7732 (mptp) REVERT: A 495 MET cc_start: 0.7615 (mmt) cc_final: 0.7382 (mmt) REVERT: A 635 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8360 (mt) REVERT: A 712 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6841 (mtt-85) REVERT: A 714 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7329 (mmm160) REVERT: A 716 ARG cc_start: 0.8015 (ttp80) cc_final: 0.6728 (tpm170) REVERT: A 717 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8054 (mmt) REVERT: B 233 LEU cc_start: 0.7592 (tt) cc_final: 0.7284 (tp) REVERT: B 279 GLN cc_start: 0.8058 (mt0) cc_final: 0.7826 (mt0) REVERT: B 280 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (tp) REVERT: B 434 LYS cc_start: 0.8323 (mtpm) cc_final: 0.7734 (mptp) REVERT: B 488 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.5916 (tpp) REVERT: B 712 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6734 (mtt-85) REVERT: B 714 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7347 (mmm160) REVERT: B 716 ARG cc_start: 0.7999 (ttp80) cc_final: 0.6528 (tpm170) REVERT: C 129 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6411 (mm-30) REVERT: C 134 GLU cc_start: 0.6619 (mp0) cc_final: 0.6345 (tp30) REVERT: C 184 LYS cc_start: 0.7032 (ttmt) cc_final: 0.6732 (tttm) REVERT: C 233 LEU cc_start: 0.7715 (tt) cc_final: 0.7442 (tp) REVERT: C 279 GLN cc_start: 0.8048 (mt0) cc_final: 0.7794 (mt0) REVERT: C 280 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8083 (tp) REVERT: C 286 GLN cc_start: 0.8364 (mt0) cc_final: 0.8052 (mm110) REVERT: C 435 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (mppt) REVERT: C 710 TRP cc_start: 0.7604 (p-90) cc_final: 0.7379 (p-90) REVERT: C 716 ARG cc_start: 0.8007 (ttp80) cc_final: 0.6604 (tpm170) REVERT: D 233 LEU cc_start: 0.7592 (tt) cc_final: 0.7307 (tp) REVERT: D 276 GLU cc_start: 0.7800 (mp0) cc_final: 0.7455 (mp0) REVERT: D 279 GLN cc_start: 0.8037 (mt0) cc_final: 0.7732 (mt0) REVERT: D 280 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8100 (tp) REVERT: D 335 THR cc_start: 0.8905 (m) cc_final: 0.8655 (p) REVERT: D 431 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7519 (mpm) REVERT: D 434 LYS cc_start: 0.8345 (mtpm) cc_final: 0.7777 (mptp) REVERT: D 488 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.5831 (tpt) REVERT: D 514 GLN cc_start: 0.7164 (pt0) cc_final: 0.6532 (mp10) REVERT: D 710 TRP cc_start: 0.7510 (p-90) cc_final: 0.7282 (p-90) REVERT: D 713 SER cc_start: 0.7941 (m) cc_final: 0.7527 (p) REVERT: D 716 ARG cc_start: 0.8004 (ttp80) cc_final: 0.6708 (tpm170) outliers start: 65 outliers final: 17 residues processed: 306 average time/residue: 0.6952 time to fit residues: 240.0707 Evaluate side-chains 280 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU 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 195 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 141 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN C 412 ASN D 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.165087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.115842 restraints weight = 22743.620| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.77 r_work: 0.2959 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22388 Z= 0.101 Angle : 0.481 5.300 29960 Z= 0.250 Chirality : 0.036 0.116 3228 Planarity : 0.003 0.040 3596 Dihedral : 21.496 151.657 4084 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.99 % Allowed : 9.40 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2476 helix: 0.65 (0.13), residues: 1588 sheet: 0.62 (0.51), residues: 112 loop : -1.25 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.015 0.001 TYR A 547 PHE 0.016 0.001 PHE A 449 TRP 0.013 0.001 TRP C 692 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (22376) covalent geometry : angle 0.48091 / 0.25 (29952) SS BOND : bond 0.00010 / 0.01 ( 4) SS BOND : angle 0.23862 / 0.17 ( 8) hydrogen bonds : bond 0.03560 / 2.33 ( 1008) hydrogen bonds : angle 3.51815 / 2.41 ( 2964) Misc. bond : bond 0.00081 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.849 Fit side-chains REVERT: A 129 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6289 (mm-30) REVERT: A 184 LYS cc_start: 0.6931 (ttmt) cc_final: 0.6596 (tttm) REVERT: A 229 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: A 233 LEU cc_start: 0.7580 (tt) cc_final: 0.7301 (tp) REVERT: A 276 GLU cc_start: 0.7666 (mp0) cc_final: 0.7348 (mp0) REVERT: A 279 GLN cc_start: 0.8040 (mt0) cc_final: 0.7767 (mt0) REVERT: A 286 GLN cc_start: 0.8342 (mt0) cc_final: 0.8054 (mm110) REVERT: A 327 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7067 (tmt-80) REVERT: A 337 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8366 (mtt-85) REVERT: A 431 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7559 (mpm) REVERT: A 434 LYS cc_start: 0.8169 (mtpm) cc_final: 0.7618 (mptm) REVERT: A 635 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 687 GLU cc_start: 0.7822 (pp20) cc_final: 0.7544 (pt0) REVERT: A 713 SER cc_start: 0.7838 (m) cc_final: 0.7372 (p) REVERT: A 714 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7572 (mtp-110) REVERT: A 716 ARG cc_start: 0.7906 (ttp80) cc_final: 0.6652 (tpm170) REVERT: A 717 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8012 (mmt) REVERT: B 233 LEU cc_start: 0.7549 (tt) cc_final: 0.7215 (tp) REVERT: B 279 GLN cc_start: 0.8067 (mt0) cc_final: 0.7745 (mt0) REVERT: B 286 GLN cc_start: 0.8374 (mt0) cc_final: 0.8016 (mm110) REVERT: B 327 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7089 (tmt-80) REVERT: B 434 LYS cc_start: 0.8188 (mtpm) cc_final: 0.7627 (mptm) REVERT: B 488 MET cc_start: 0.6965 (tpp) cc_final: 0.6582 (tpp) REVERT: B 687 GLU cc_start: 0.7830 (pp20) cc_final: 0.7547 (pt0) REVERT: B 706 MET cc_start: 0.7732 (mtm) cc_final: 0.7527 (mtp) REVERT: B 713 SER cc_start: 0.7770 (m) cc_final: 0.7270 (p) REVERT: B 716 ARG cc_start: 0.7912 (ttp80) cc_final: 0.6499 (tpm170) REVERT: C 129 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6327 (mm-30) REVERT: C 233 LEU cc_start: 0.7719 (tt) cc_final: 0.7355 (tp) REVERT: C 279 GLN cc_start: 0.8063 (mt0) cc_final: 0.7782 (mt0) REVERT: C 286 GLN cc_start: 0.8369 (mt0) cc_final: 0.8099 (mm110) REVERT: C 327 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6975 (tmt-80) REVERT: C 371 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7617 (mmm-85) REVERT: C 435 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8120 (mppt) REVERT: C 687 GLU cc_start: 0.7824 (pp20) cc_final: 0.7542 (pt0) REVERT: C 706 MET cc_start: 0.7757 (mtm) cc_final: 0.7549 (mtp) REVERT: C 710 TRP cc_start: 0.7536 (p-90) cc_final: 0.7278 (p-90) REVERT: C 713 SER cc_start: 0.7857 (m) cc_final: 0.7371 (p) REVERT: C 716 ARG cc_start: 0.7882 (ttp80) cc_final: 0.6547 (tpm170) REVERT: D 233 LEU cc_start: 0.7498 (tt) cc_final: 0.7193 (tp) REVERT: D 276 GLU cc_start: 0.7644 (mp0) cc_final: 0.7331 (mp0) REVERT: D 279 GLN cc_start: 0.8025 (mt0) cc_final: 0.7759 (mt0) REVERT: D 286 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7979 (mm110) REVERT: D 335 THR cc_start: 0.8822 (m) cc_final: 0.8601 (p) REVERT: D 431 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8065 (mmp) REVERT: D 434 LYS cc_start: 0.8199 (mtpm) cc_final: 0.7628 (mptm) REVERT: D 488 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.5925 (tpt) REVERT: D 514 GLN cc_start: 0.6930 (pt0) cc_final: 0.6245 (mp10) REVERT: D 687 GLU cc_start: 0.7815 (pp20) cc_final: 0.7504 (pt0) REVERT: D 698 ARG cc_start: 0.8536 (ttt90) cc_final: 0.7420 (mtm-85) REVERT: D 710 TRP cc_start: 0.7498 (p-90) cc_final: 0.7282 (p-90) REVERT: D 713 SER cc_start: 0.7822 (m) cc_final: 0.7439 (p) REVERT: D 716 ARG cc_start: 0.7891 (ttp80) cc_final: 0.6622 (tpm170) outliers start: 44 outliers final: 8 residues processed: 306 average time/residue: 0.7157 time to fit residues: 246.8663 Evaluate side-chains 275 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 163 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 110 optimal weight: 0.0050 chunk 68 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 203 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 412 ASN C 227 GLN D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.117361 restraints weight = 22658.139| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.77 r_work: 0.2974 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 22388 Z= 0.091 Angle : 0.457 8.190 29960 Z= 0.237 Chirality : 0.035 0.117 3228 Planarity : 0.003 0.038 3596 Dihedral : 20.387 154.880 4084 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.90 % Allowed : 10.13 % Favored : 87.97 % 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: 0.79 (0.17), residues: 2476 helix: 1.32 (0.13), residues: 1584 sheet: 0.81 (0.51), residues: 112 loop : -1.16 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.015 0.001 TYR A 547 PHE 0.019 0.001 PHE A 449 TRP 0.011 0.001 TRP B 692 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (22376) covalent geometry : angle 0.45729 / 0.24 (29952) SS BOND : bond 0.00012 / 0.01 ( 4) SS BOND : angle 0.21138 / 0.15 ( 8) hydrogen bonds : bond 0.03193 / 2.08 ( 1008) hydrogen bonds : angle 3.35146 / 2.29 ( 2964) Misc. bond : bond 0.00075 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.850 Fit side-chains REVERT: A 129 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6285 (mm-30) REVERT: A 229 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: A 233 LEU cc_start: 0.7570 (tt) cc_final: 0.7230 (tp) REVERT: A 276 GLU cc_start: 0.7681 (mp0) cc_final: 0.7364 (mp0) REVERT: A 279 GLN cc_start: 0.8019 (mt0) cc_final: 0.7711 (mt0) REVERT: A 286 GLN cc_start: 0.8356 (mt0) cc_final: 0.8080 (mm110) REVERT: A 327 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7057 (tmt-80) REVERT: A 431 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7555 (mpm) REVERT: A 434 LYS cc_start: 0.8240 (mtpm) cc_final: 0.7668 (mptm) REVERT: A 514 GLN cc_start: 0.6805 (pt0) cc_final: 0.6176 (mp10) REVERT: A 635 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 687 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: A 698 ARG cc_start: 0.8497 (ttt90) cc_final: 0.7363 (mtm-85) REVERT: A 713 SER cc_start: 0.7787 (m) cc_final: 0.7348 (p) REVERT: A 714 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7667 (mtp-110) REVERT: A 716 ARG cc_start: 0.7870 (ttp80) cc_final: 0.6544 (tpm170) REVERT: A 717 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7889 (mmt) REVERT: B 129 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6245 (mm-30) REVERT: B 229 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: B 233 LEU cc_start: 0.7515 (tt) cc_final: 0.7169 (tp) REVERT: B 279 GLN cc_start: 0.8045 (mt0) cc_final: 0.7746 (mt0) REVERT: B 286 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8072 (mm110) REVERT: B 327 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7054 (tmt-80) REVERT: B 434 LYS cc_start: 0.8203 (mtpm) cc_final: 0.7628 (mptm) REVERT: B 488 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6580 (tpp) REVERT: B 687 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: B 698 ARG cc_start: 0.8492 (ttt90) cc_final: 0.7380 (mtm-85) REVERT: B 713 SER cc_start: 0.7695 (m) cc_final: 0.7279 (p) REVERT: B 714 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7509 (mtp-110) REVERT: B 716 ARG cc_start: 0.7808 (ttp80) cc_final: 0.6442 (tpm170) REVERT: C 129 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6275 (mm-30) REVERT: C 134 GLU cc_start: 0.6633 (mp0) cc_final: 0.6314 (tp30) REVERT: C 233 LEU cc_start: 0.7598 (tt) cc_final: 0.7235 (tp) REVERT: C 286 GLN cc_start: 0.8346 (mt0) cc_final: 0.8107 (mm110) REVERT: C 327 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7169 (tmt-80) REVERT: C 371 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7627 (mmm-85) REVERT: C 435 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8009 (mppt) REVERT: C 687 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: C 698 ARG cc_start: 0.8496 (ttt90) cc_final: 0.7361 (mtm-85) REVERT: C 710 TRP cc_start: 0.7472 (p-90) cc_final: 0.7270 (p-90) REVERT: C 713 SER cc_start: 0.7813 (m) cc_final: 0.7360 (p) REVERT: C 714 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7755 (mtp-110) REVERT: C 716 ARG cc_start: 0.7829 (ttp80) cc_final: 0.6548 (tpm170) REVERT: D 229 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: D 233 LEU cc_start: 0.7520 (tt) cc_final: 0.7223 (tp) REVERT: D 276 GLU cc_start: 0.7670 (mp0) cc_final: 0.7366 (mp0) REVERT: D 279 GLN cc_start: 0.7996 (mt0) cc_final: 0.7732 (mt0) REVERT: D 286 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7990 (mm110) REVERT: D 327 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7095 (tmt-80) REVERT: D 335 THR cc_start: 0.8817 (m) cc_final: 0.8566 (p) REVERT: D 431 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8073 (mmp) REVERT: D 434 LYS cc_start: 0.8232 (mtpm) cc_final: 0.7634 (mptm) REVERT: D 488 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6474 (tpp) REVERT: D 514 GLN cc_start: 0.6845 (pt0) cc_final: 0.6223 (mp10) REVERT: D 687 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: D 698 ARG cc_start: 0.8500 (ttt90) cc_final: 0.7367 (mtm-85) REVERT: D 713 SER cc_start: 0.7865 (m) cc_final: 0.7528 (p) REVERT: D 716 ARG cc_start: 0.7847 (ttp80) cc_final: 0.6591 (tpm170) outliers start: 42 outliers final: 6 residues processed: 279 average time/residue: 0.7162 time to fit residues: 226.5134 Evaluate side-chains 283 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 687 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 244 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN D 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.165081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115955 restraints weight = 22743.389| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.77 r_work: 0.3072 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22388 Z= 0.101 Angle : 0.467 6.859 29960 Z= 0.241 Chirality : 0.036 0.114 3228 Planarity : 0.003 0.036 3596 Dihedral : 19.977 154.410 4084 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 10.53 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2476 helix: 1.58 (0.13), residues: 1580 sheet: 0.88 (0.51), residues: 112 loop : -1.06 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.017 0.001 TYR A 547 PHE 0.017 0.001 PHE D 449 TRP 0.011 0.001 TRP A 692 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (22376) covalent geometry : angle 0.46731 / 0.24 (29952) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 0.25229 / 0.18 ( 8) hydrogen bonds : bond 0.03366 / 2.20 ( 1008) hydrogen bonds : angle 3.32792 / 2.28 ( 2964) Misc. bond : bond 0.00075 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.711 Fit side-chains REVERT: A 129 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6366 (mm-30) REVERT: A 134 GLU cc_start: 0.6688 (mp0) cc_final: 0.6346 (tp30) REVERT: A 184 LYS cc_start: 0.6989 (ttmt) cc_final: 0.6685 (tttm) REVERT: A 214 GLU cc_start: 0.7977 (tt0) cc_final: 0.7736 (tt0) REVERT: A 229 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: A 233 LEU cc_start: 0.7682 (tt) cc_final: 0.7399 (tp) REVERT: A 276 GLU cc_start: 0.7662 (mp0) cc_final: 0.7377 (mp0) REVERT: A 286 GLN cc_start: 0.8354 (mt0) cc_final: 0.8139 (mm110) REVERT: A 327 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7140 (tmt-80) REVERT: A 431 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7534 (mpm) REVERT: A 434 LYS cc_start: 0.8220 (mtpm) cc_final: 0.7663 (mptm) REVERT: A 635 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 687 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: A 698 ARG cc_start: 0.8508 (ttt90) cc_final: 0.7398 (mtm-85) REVERT: A 713 SER cc_start: 0.7844 (m) cc_final: 0.7427 (p) REVERT: A 714 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7690 (mtp-110) REVERT: A 716 ARG cc_start: 0.7872 (ttp80) cc_final: 0.6643 (tpm170) REVERT: A 717 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7927 (mmt) REVERT: B 129 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6328 (mm-30) REVERT: B 184 LYS cc_start: 0.7024 (ttmt) cc_final: 0.6723 (tttm) REVERT: B 229 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7067 (m-30) REVERT: B 233 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7374 (tp) REVERT: B 286 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8129 (mm110) REVERT: B 327 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7101 (tmt-80) REVERT: B 434 LYS cc_start: 0.8205 (mtpm) cc_final: 0.7636 (mptm) REVERT: B 435 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8084 (mppt) REVERT: B 488 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6712 (tpp) REVERT: B 687 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: B 698 ARG cc_start: 0.8523 (ttt90) cc_final: 0.7419 (mtm-85) REVERT: B 713 SER cc_start: 0.7744 (m) cc_final: 0.7321 (p) REVERT: B 714 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7585 (mtp-110) REVERT: B 716 ARG cc_start: 0.7861 (ttp80) cc_final: 0.6582 (tpm170) REVERT: C 129 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6372 (mm-30) REVERT: C 134 GLU cc_start: 0.6716 (mp0) cc_final: 0.6413 (tp30) REVERT: C 233 LEU cc_start: 0.7683 (tt) cc_final: 0.7316 (tp) REVERT: C 327 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7226 (tmt-80) REVERT: C 371 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7706 (mmm-85) REVERT: C 435 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8093 (mppt) REVERT: C 687 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: C 698 ARG cc_start: 0.8507 (ttt90) cc_final: 0.7398 (mtm-85) REVERT: C 713 SER cc_start: 0.7848 (m) cc_final: 0.7388 (p) REVERT: C 714 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7784 (mtp-110) REVERT: C 716 ARG cc_start: 0.7885 (ttp80) cc_final: 0.6664 (tpm170) REVERT: D 129 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6364 (mm-30) REVERT: D 229 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: D 233 LEU cc_start: 0.7589 (tt) cc_final: 0.7239 (tp) REVERT: D 276 GLU cc_start: 0.7656 (mp0) cc_final: 0.7376 (mp0) REVERT: D 286 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (mm110) REVERT: D 327 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7091 (tmt-80) REVERT: D 431 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7455 (mpm) REVERT: D 434 LYS cc_start: 0.8233 (mtpm) cc_final: 0.7670 (mptm) REVERT: D 488 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6513 (tpp) REVERT: D 514 GLN cc_start: 0.6901 (pt0) cc_final: 0.6281 (mp10) REVERT: D 687 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: D 698 ARG cc_start: 0.8505 (ttt90) cc_final: 0.7392 (mtm-85) REVERT: D 713 SER cc_start: 0.7905 (m) cc_final: 0.7583 (p) REVERT: D 716 ARG cc_start: 0.7898 (ttp80) cc_final: 0.6725 (tpm170) outliers start: 40 outliers final: 11 residues processed: 280 average time/residue: 0.6690 time to fit residues: 211.5545 Evaluate side-chains 297 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 687 GLU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 23 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 412 ASN C 412 ASN ** C 430 HIS ** 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 = 0.3750 r_free = 0.3750 target = 0.163593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.114439 restraints weight = 22636.214| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.76 r_work: 0.2925 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22388 Z= 0.122 Angle : 0.497 7.219 29960 Z= 0.254 Chirality : 0.038 0.137 3228 Planarity : 0.003 0.038 3596 Dihedral : 19.801 148.931 4084 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.03 % Allowed : 10.49 % Favored : 87.48 % 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: 1.13 (0.18), residues: 2476 helix: 1.58 (0.13), residues: 1592 sheet: 0.94 (0.51), residues: 112 loop : -1.03 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 327 TYR 0.016 0.002 TYR C 547 PHE 0.015 0.001 PHE A 449 TRP 0.012 0.001 TRP D 692 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (22376) covalent geometry : angle 0.49727 / 0.25 (29952) SS BOND : bond 0.00034 / 0.02 ( 4) SS BOND : angle 0.35901 / 0.25 ( 8) hydrogen bonds : bond 0.03729 / 2.44 ( 1008) hydrogen bonds : angle 3.42631 / 2.35 ( 2964) Misc. bond : bond 0.00073 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.676 Fit side-chains REVERT: A 129 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6337 (mm-30) REVERT: A 134 GLU cc_start: 0.6584 (mp0) cc_final: 0.6285 (tp30) REVERT: A 214 GLU cc_start: 0.8139 (tt0) cc_final: 0.7894 (tt0) REVERT: A 233 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7282 (tp) REVERT: A 276 GLU cc_start: 0.7673 (mp0) cc_final: 0.7354 (mp0) REVERT: A 280 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 286 GLN cc_start: 0.8379 (mt0) cc_final: 0.8124 (mm110) REVERT: A 327 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7135 (tmt-80) REVERT: A 431 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7504 (mpm) REVERT: A 434 LYS cc_start: 0.8244 (mtpm) cc_final: 0.7669 (mptm) REVERT: A 635 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 687 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: A 713 SER cc_start: 0.7777 (m) cc_final: 0.7351 (p) REVERT: A 714 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7675 (mtp-110) REVERT: A 716 ARG cc_start: 0.7823 (ttp80) cc_final: 0.6538 (tpm170) REVERT: B 129 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6277 (mm-30) REVERT: B 184 LYS cc_start: 0.6913 (ttmt) cc_final: 0.6584 (tttm) REVERT: B 214 GLU cc_start: 0.8141 (tt0) cc_final: 0.7892 (tt0) REVERT: B 233 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7310 (tp) REVERT: B 280 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7919 (tp) REVERT: B 286 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8132 (mm110) REVERT: B 327 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7131 (tmt-80) REVERT: B 431 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7458 (mpm) REVERT: B 434 LYS cc_start: 0.8241 (mtpm) cc_final: 0.7638 (mptm) REVERT: B 435 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8226 (mppt) REVERT: B 488 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6641 (tpp) REVERT: B 698 ARG cc_start: 0.8582 (ttt90) cc_final: 0.7450 (mtm-85) REVERT: B 713 SER cc_start: 0.7729 (m) cc_final: 0.7308 (p) REVERT: B 714 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7563 (mtp-110) REVERT: B 716 ARG cc_start: 0.7867 (ttp80) cc_final: 0.6557 (tpm170) REVERT: C 129 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6316 (mm-30) REVERT: C 134 GLU cc_start: 0.6646 (mp0) cc_final: 0.6337 (tp30) REVERT: C 233 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7249 (tp) REVERT: C 280 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7955 (tp) REVERT: C 371 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7669 (mmm-85) REVERT: C 435 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8152 (mppt) REVERT: C 713 SER cc_start: 0.7806 (m) cc_final: 0.7338 (p) REVERT: C 714 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7781 (mtp-110) REVERT: C 716 ARG cc_start: 0.7877 (ttp80) cc_final: 0.6584 (tpm170) REVERT: D 129 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6308 (mm-30) REVERT: D 214 GLU cc_start: 0.8119 (tt0) cc_final: 0.7888 (tt0) REVERT: D 233 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7251 (tp) REVERT: D 276 GLU cc_start: 0.7677 (mp0) cc_final: 0.7360 (mp0) REVERT: D 280 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7902 (tp) REVERT: D 286 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (mm110) REVERT: D 431 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7457 (mpm) REVERT: D 434 LYS cc_start: 0.8237 (mtpm) cc_final: 0.7651 (mptm) REVERT: D 488 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.5840 (tpp) REVERT: D 687 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: D 713 SER cc_start: 0.7843 (m) cc_final: 0.7510 (p) REVERT: D 716 ARG cc_start: 0.7870 (ttp80) cc_final: 0.6676 (tpm170) outliers start: 45 outliers final: 13 residues processed: 279 average time/residue: 0.6813 time to fit residues: 215.8176 Evaluate side-chains 299 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 687 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 412 ASN C 412 ASN ** C 430 HIS ** 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 = 0.3723 r_free = 0.3723 target = 0.161156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111941 restraints weight = 22613.865| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.75 r_work: 0.2903 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22388 Z= 0.165 Angle : 0.558 6.769 29960 Z= 0.283 Chirality : 0.040 0.180 3228 Planarity : 0.003 0.040 3596 Dihedral : 19.980 140.602 4084 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.54 % Favored : 97.29 % Rotamer: Outliers : 1.99 % Allowed : 11.08 % Favored : 86.93 % 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: 0.97 (0.17), residues: 2476 helix: 1.42 (0.13), residues: 1588 sheet: 0.91 (0.51), residues: 112 loop : -1.01 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 327 TYR 0.019 0.002 TYR C 547 PHE 0.014 0.002 PHE A 449 TRP 0.014 0.001 TRP A 692 HIS 0.008 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (22376) covalent geometry : angle 0.55770 / 0.28 (29952) SS BOND : bond 0.00040 / 0.02 ( 4) SS BOND : angle 0.47855 / 0.34 ( 8) hydrogen bonds : bond 0.04291 / 2.82 ( 1008) hydrogen bonds : angle 3.65042 / 2.50 ( 2964) Misc. bond : bond 0.00077 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.648 Fit side-chains REVERT: A 129 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6346 (mm-30) REVERT: A 134 GLU cc_start: 0.6624 (mp0) cc_final: 0.6311 (tp30) REVERT: A 184 LYS cc_start: 0.7038 (ttmt) cc_final: 0.6658 (tttm) REVERT: A 185 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6470 (mp0) REVERT: A 233 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7401 (tp) REVERT: A 276 GLU cc_start: 0.7672 (mp0) cc_final: 0.7342 (mp0) REVERT: A 280 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7923 (tp) REVERT: A 286 GLN cc_start: 0.8395 (mt0) cc_final: 0.8135 (mm110) REVERT: A 431 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7540 (mpm) REVERT: A 434 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7679 (mptm) REVERT: A 635 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 687 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: A 713 SER cc_start: 0.7789 (m) cc_final: 0.7363 (p) REVERT: A 716 ARG cc_start: 0.7804 (ttp80) cc_final: 0.6519 (tpm170) REVERT: A 717 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8254 (mmt) REVERT: B 129 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6346 (mm-30) REVERT: B 134 GLU cc_start: 0.6490 (mp0) cc_final: 0.6115 (tp30) REVERT: B 233 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7310 (tp) REVERT: B 280 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 286 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8181 (mm110) REVERT: B 327 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7188 (tmt-80) REVERT: B 431 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7465 (mpm) REVERT: B 434 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7653 (mptm) REVERT: B 435 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8217 (mppt) REVERT: B 488 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.5962 (tpp) REVERT: B 713 SER cc_start: 0.7787 (m) cc_final: 0.7357 (p) REVERT: B 714 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7544 (mtp-110) REVERT: B 716 ARG cc_start: 0.7922 (ttp80) cc_final: 0.6513 (tpm170) REVERT: C 129 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6375 (mm-30) REVERT: C 134 GLU cc_start: 0.6758 (mp0) cc_final: 0.6431 (tp30) REVERT: C 185 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6461 (mp0) REVERT: C 233 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7352 (tp) REVERT: C 280 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 289 ILE cc_start: 0.8686 (mt) cc_final: 0.8336 (mp) REVERT: C 371 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7635 (mmm-85) REVERT: C 435 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8210 (mppt) REVERT: C 713 SER cc_start: 0.7834 (m) cc_final: 0.7371 (p) REVERT: C 714 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7760 (mtp-110) REVERT: C 716 ARG cc_start: 0.7905 (ttp80) cc_final: 0.6599 (tpm170) REVERT: D 129 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6354 (mm-30) REVERT: D 134 GLU cc_start: 0.6493 (mp0) cc_final: 0.6099 (tp30) REVERT: D 233 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7323 (tp) REVERT: D 276 GLU cc_start: 0.7688 (mp0) cc_final: 0.7370 (mp0) REVERT: D 286 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8123 (mm110) REVERT: D 431 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7473 (mpm) REVERT: D 434 LYS cc_start: 0.8303 (mtpm) cc_final: 0.7712 (mptm) REVERT: D 488 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.5844 (tpp) REVERT: D 713 SER cc_start: 0.7843 (m) cc_final: 0.7504 (p) REVERT: D 716 ARG cc_start: 0.7903 (ttp80) cc_final: 0.6670 (tpm170) outliers start: 44 outliers final: 17 residues processed: 281 average time/residue: 0.6488 time to fit residues: 206.1074 Evaluate side-chains 302 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 18 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 0.3980 chunk 8 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN C 279 GLN 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 = 0.3733 r_free = 0.3733 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112998 restraints weight = 22730.972| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.76 r_work: 0.2921 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22388 Z= 0.132 Angle : 0.512 6.944 29960 Z= 0.262 Chirality : 0.038 0.147 3228 Planarity : 0.003 0.038 3596 Dihedral : 19.710 135.194 4084 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.76 % Allowed : 11.93 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.17), residues: 2476 helix: 1.55 (0.13), residues: 1584 sheet: 0.96 (0.51), residues: 112 loop : -1.01 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.021 0.002 TYR A 547 PHE 0.014 0.001 PHE A 449 TRP 0.013 0.001 TRP A 692 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (22376) covalent geometry : angle 0.51220 / 0.26 (29952) SS BOND : bond 0.00034 / 0.02 ( 4) SS BOND : angle 0.41776 / 0.29 ( 8) hydrogen bonds : bond 0.03806 / 2.49 ( 1008) hydrogen bonds : angle 3.52958 / 2.42 ( 2964) Misc. bond : bond 0.00066 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.645 Fit side-chains REVERT: A 129 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6384 (mm-30) REVERT: A 134 GLU cc_start: 0.6686 (mp0) cc_final: 0.6375 (tp30) REVERT: A 185 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6496 (mp0) REVERT: A 233 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7337 (tp) REVERT: A 276 GLU cc_start: 0.7625 (mp0) cc_final: 0.7305 (mp0) REVERT: A 279 GLN cc_start: 0.7936 (mt0) cc_final: 0.7708 (mt0) REVERT: A 286 GLN cc_start: 0.8392 (mt0) cc_final: 0.8166 (mm110) REVERT: A 289 ILE cc_start: 0.8609 (mt) cc_final: 0.8259 (mp) REVERT: A 327 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7129 (tmt-80) REVERT: A 431 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7486 (mpm) REVERT: A 434 LYS cc_start: 0.8246 (mtpm) cc_final: 0.7664 (mptm) REVERT: A 635 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 713 SER cc_start: 0.7749 (m) cc_final: 0.7340 (p) REVERT: A 716 ARG cc_start: 0.7796 (ttp80) cc_final: 0.6497 (tpm170) REVERT: B 129 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6419 (mm-30) REVERT: B 134 GLU cc_start: 0.6589 (mp0) cc_final: 0.6290 (tp30) REVERT: B 185 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6467 (mp0) REVERT: B 233 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7338 (tp) REVERT: B 286 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8199 (mm110) REVERT: B 327 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7147 (tmt-80) REVERT: B 431 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7467 (mpm) REVERT: B 434 LYS cc_start: 0.8256 (mtpm) cc_final: 0.7643 (mptm) REVERT: B 435 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8184 (mppt) REVERT: B 488 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.5981 (tpp) REVERT: B 713 SER cc_start: 0.7746 (m) cc_final: 0.7324 (p) REVERT: B 714 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7568 (mtp-110) REVERT: B 716 ARG cc_start: 0.7853 (ttp80) cc_final: 0.6451 (tpm170) REVERT: C 129 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6395 (mm-30) REVERT: C 134 GLU cc_start: 0.6805 (mp0) cc_final: 0.6467 (tp30) REVERT: C 233 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7345 (tp) REVERT: C 289 ILE cc_start: 0.8669 (mt) cc_final: 0.8323 (mp) REVERT: C 371 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7674 (mmm-85) REVERT: C 435 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8209 (mppt) REVERT: C 713 SER cc_start: 0.7794 (m) cc_final: 0.7338 (p) REVERT: C 714 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7763 (mtp-110) REVERT: C 716 ARG cc_start: 0.7879 (ttp80) cc_final: 0.6583 (tpm170) REVERT: D 129 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6400 (mm-30) REVERT: D 134 GLU cc_start: 0.6581 (mp0) cc_final: 0.6215 (tp30) REVERT: D 185 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6474 (mp0) REVERT: D 233 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7337 (tp) REVERT: D 276 GLU cc_start: 0.7658 (mp0) cc_final: 0.7354 (mp0) REVERT: D 280 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8013 (tp) REVERT: D 286 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8167 (mm110) REVERT: D 431 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7443 (mpm) REVERT: D 434 LYS cc_start: 0.8255 (mtpm) cc_final: 0.7657 (mptm) REVERT: D 488 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.5886 (tpp) REVERT: D 713 SER cc_start: 0.7876 (m) cc_final: 0.7543 (p) REVERT: D 716 ARG cc_start: 0.7888 (ttp80) cc_final: 0.6657 (tpm170) outliers start: 39 outliers final: 16 residues processed: 281 average time/residue: 0.6124 time to fit residues: 195.2362 Evaluate side-chains 293 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 286 GLN Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 32 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 279 GLN 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 = 0.3748 r_free = 0.3748 target = 0.163404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.114582 restraints weight = 22820.529| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.76 r_work: 0.3056 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22388 Z= 0.106 Angle : 0.480 7.295 29960 Z= 0.247 Chirality : 0.037 0.122 3228 Planarity : 0.003 0.037 3596 Dihedral : 19.299 130.691 4084 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 12.34 % Favored : 86.08 % 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: 1.28 (0.18), residues: 2476 helix: 1.68 (0.13), residues: 1592 sheet: 1.04 (0.51), residues: 112 loop : -0.93 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.024 0.002 TYR A 547 PHE 0.014 0.001 PHE A 449 TRP 0.012 0.001 TRP D 692 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (22376) covalent geometry : angle 0.48034 / 0.25 (29952) SS BOND : bond 0.00013 / 0.01 ( 4) SS BOND : angle 0.34314 / 0.24 ( 8) hydrogen bonds : bond 0.03433 / 2.24 ( 1008) hydrogen bonds : angle 3.41862 / 2.34 ( 2964) Misc. bond : bond 0.00050 / 0.03 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.935 Fit side-chains REVERT: A 129 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6425 (mm-30) REVERT: A 134 GLU cc_start: 0.6751 (mp0) cc_final: 0.6434 (tp30) REVERT: A 185 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6374 (mp0) REVERT: A 233 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7378 (tp) REVERT: A 276 GLU cc_start: 0.7581 (mp0) cc_final: 0.7311 (mp0) REVERT: A 286 GLN cc_start: 0.8380 (mt0) cc_final: 0.8170 (mm110) REVERT: A 289 ILE cc_start: 0.8578 (mt) cc_final: 0.8241 (mp) REVERT: A 327 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7143 (tmt-80) REVERT: A 431 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7537 (mpm) REVERT: A 434 LYS cc_start: 0.8232 (mtpm) cc_final: 0.7654 (mptm) REVERT: A 635 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 698 ARG cc_start: 0.8539 (ttt90) cc_final: 0.7422 (mtm-85) REVERT: A 713 SER cc_start: 0.7771 (m) cc_final: 0.7393 (p) REVERT: A 716 ARG cc_start: 0.7718 (ttp80) cc_final: 0.6530 (tpm170) REVERT: A 717 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: B 129 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6451 (mm-30) REVERT: B 134 GLU cc_start: 0.6660 (mp0) cc_final: 0.6314 (tp30) REVERT: B 185 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6499 (mp0) REVERT: B 233 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7350 (tp) REVERT: B 327 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7139 (tmt-80) REVERT: B 431 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7479 (mpm) REVERT: B 434 LYS cc_start: 0.8231 (mtpm) cc_final: 0.7642 (mptm) REVERT: B 435 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8175 (mppt) REVERT: B 488 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6671 (tpp) REVERT: B 698 ARG cc_start: 0.8555 (ttt90) cc_final: 0.7441 (mtm-85) REVERT: B 713 SER cc_start: 0.7768 (m) cc_final: 0.7377 (p) REVERT: B 714 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (mtp-110) REVERT: B 716 ARG cc_start: 0.7812 (ttp80) cc_final: 0.6467 (tpm170) REVERT: C 129 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6423 (mm-30) REVERT: C 134 GLU cc_start: 0.6865 (mp0) cc_final: 0.6549 (tp30) REVERT: C 233 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7365 (tp) REVERT: C 279 GLN cc_start: 0.7907 (mt0) cc_final: 0.7682 (mt0) REVERT: C 289 ILE cc_start: 0.8656 (mt) cc_final: 0.8322 (mp) REVERT: C 327 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7071 (tmt-80) REVERT: C 371 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7717 (mmm-85) REVERT: C 435 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8148 (mppt) REVERT: C 713 SER cc_start: 0.7818 (m) cc_final: 0.7370 (p) REVERT: C 714 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (mtp-110) REVERT: C 716 ARG cc_start: 0.7882 (ttp80) cc_final: 0.6635 (tpm170) REVERT: D 129 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6439 (mm-30) REVERT: D 134 GLU cc_start: 0.6721 (mp0) cc_final: 0.6338 (tp30) REVERT: D 184 LYS cc_start: 0.7077 (ttmt) cc_final: 0.6670 (tttm) REVERT: D 185 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6531 (mp0) REVERT: D 233 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7419 (tp) REVERT: D 276 GLU cc_start: 0.7602 (mp0) cc_final: 0.7323 (mp0) REVERT: D 327 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7181 (tmt-80) REVERT: D 431 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7457 (mpm) REVERT: D 434 LYS cc_start: 0.8216 (mtpm) cc_final: 0.7648 (mptm) REVERT: D 488 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.5871 (tpp) REVERT: D 713 SER cc_start: 0.7897 (m) cc_final: 0.7570 (p) REVERT: D 716 ARG cc_start: 0.7838 (ttp80) cc_final: 0.6662 (tpm170) outliers start: 35 outliers final: 11 residues processed: 279 average time/residue: 0.6899 time to fit residues: 218.5847 Evaluate side-chains 291 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 714 ARG Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 655 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 200 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 12 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 279 GLN C 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.164962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116324 restraints weight = 22835.672| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.77 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22388 Z= 0.091 Angle : 0.465 8.403 29960 Z= 0.240 Chirality : 0.036 0.114 3228 Planarity : 0.003 0.036 3596 Dihedral : 18.820 126.065 4084 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.36 % Allowed : 12.70 % Favored : 85.94 % 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: 1.46 (0.18), residues: 2476 helix: 1.76 (0.13), residues: 1608 sheet: 1.12 (0.52), residues: 112 loop : -0.78 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.021 0.001 TYR C 547 PHE 0.015 0.001 PHE B 316 TRP 0.010 0.001 TRP B 739 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (22376) covalent geometry : angle 0.46459 / 0.24 (29952) SS BOND : bond 0.00014 / 0.01 ( 4) SS BOND : angle 0.26367 / 0.18 ( 8) hydrogen bonds : bond 0.03112 / 2.03 ( 1008) hydrogen bonds : angle 3.35900 / 2.29 ( 2964) Misc. bond : bond 0.00047 / 0.03 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9621.35 seconds wall clock time: 164 minutes 6.18 seconds (9846.18 seconds total)