Starting phenix.real_space_refine on Sun Oct 12 06:44:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6l_42995/10_2025/8v6l_42995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6l_42995/10_2025/8v6l_42995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v6l_42995/10_2025/8v6l_42995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6l_42995/10_2025/8v6l_42995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v6l_42995/10_2025/8v6l_42995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6l_42995/10_2025/8v6l_42995.map" } resolution = 3.68 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= 0.004 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 136 5.16 5 Na 3 4.78 5 C 14724 2.51 5 N 3552 2.21 5 O 3952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22387 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "C" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "D" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 283 Unusual residues: {' NA': 2, 'I8E': 1, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 334 Unusual residues: {' NA': 1, 'I8E': 1, 'POV': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 281 Unusual residues: {'I8E': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'I8E': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.33, per 1000 atoms: 0.24 Number of scatterers: 22387 At special positions: 0 Unit cell: (136.95, 136.95, 124.5, 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 136 16.00 P 20 15.00 Na 3 11.00 O 3952 8.00 N 3552 7.00 C 14724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 64.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.510A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 152 through 163 removed outlier: 4.516A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.886A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.610A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.570A pdb=" N THR A 336 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.568A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 437 through 458 Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.755A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 543 removed outlier: 3.962A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 4.058A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.658A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.949A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 609 removed outlier: 4.340A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.767A pdb=" N ASP A 615 " --> pdb=" O CYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 669 through 687 removed outlier: 3.805A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 4.182A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.545A pdb=" N TRP A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 131 through 147 Processing helix chain 'B' and resid 152 through 163 removed outlier: 4.516A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.889A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.623A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.577A pdb=" N THR B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.572A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 437 through 458 Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.759A pdb=" N LEU B 485 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 519 through 543 removed outlier: 3.956A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.075A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.675A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 573 Processing helix chain 'B' and resid 574 through 586 removed outlier: 4.104A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 609 removed outlier: 4.344A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.775A pdb=" N ASP B 615 " --> pdb=" O CYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 651 through 666 Processing helix chain 'B' and resid 669 through 687 removed outlier: 3.872A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 4.193A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.521A pdb=" N TRP B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 131 through 147 Processing helix chain 'C' and resid 152 through 163 removed outlier: 4.519A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.887A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.613A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.575A pdb=" N THR C 336 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.566A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 437 through 458 Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.763A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 519 through 543 removed outlier: 3.968A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 4.072A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.667A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 573 Processing helix chain 'C' and resid 574 through 584 removed outlier: 4.022A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 609 removed outlier: 4.345A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.770A pdb=" N ASP C 615 " --> pdb=" O CYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 651 through 666 Processing helix chain 'C' and resid 669 through 687 removed outlier: 3.831A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 4.184A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.544A pdb=" N TRP C 742 " --> pdb=" O LYS C 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 152 through 162 removed outlier: 4.511A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.892A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.614A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.579A pdb=" N THR D 336 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.569A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 437 through 458 Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.766A pdb=" N LEU D 485 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 519 through 543 removed outlier: 3.969A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.076A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.670A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 573 Processing helix chain 'D' and resid 574 through 584 removed outlier: 4.021A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 609 removed outlier: 4.341A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 removed outlier: 3.788A pdb=" N ASP D 615 " --> pdb=" O CYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 651 through 666 Processing helix chain 'D' and resid 669 through 687 removed outlier: 3.827A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 4.184A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.529A pdb=" N TRP D 742 " --> pdb=" O LYS D 738 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.722A pdb=" N TYR A 390 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.723A pdb=" N TYR B 390 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 385 through 386 Processing sheet with id=AA6, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.721A pdb=" N TYR C 390 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 385 through 386 Processing sheet with id=AA8, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.716A pdb=" N TYR D 390 " --> pdb=" O LEU D 732 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 3039 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: 3.60 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3787 1.33 - 1.45: 5727 1.45 - 1.57: 13062 1.57 - 1.70: 40 1.70 - 1.82: 224 Bond restraints: 22840 Sorted by residual: bond pdb=" O12 POV C 903 " pdb=" P POV C 903 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" O12 POV B 901 " pdb=" P POV B 901 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" O12 POV A 902 " pdb=" P POV A 902 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" O12 POV B 907 " pdb=" P POV B 907 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O12 POV D 903 " pdb=" P POV D 903 " ideal model delta sigma weight residual 1.657 1.596 0.061 2.00e-02 2.50e+03 9.45e+00 ... (remaining 22835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 28457 1.07 - 2.14: 1751 2.14 - 3.21: 353 3.21 - 4.28: 124 4.28 - 5.34: 27 Bond angle restraints: 30712 Sorted by residual: angle pdb=" N ARG D 462 " pdb=" CA ARG D 462 " pdb=" C ARG D 462 " ideal model delta sigma weight residual 109.42 104.30 5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" N CYS A 619 " pdb=" CA CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N CYS C 619 " pdb=" CA CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sigma weight residual 114.17 110.53 3.64 1.14e+00 7.69e-01 1.02e+01 angle pdb=" N CYS B 619 " pdb=" CA CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sigma weight residual 114.17 110.60 3.57 1.14e+00 7.69e-01 9.79e+00 angle pdb=" N ARG C 462 " pdb=" CA ARG C 462 " pdb=" C ARG C 462 " ideal model delta sigma weight residual 109.44 104.45 4.99 1.81e+00 3.05e-01 7.60e+00 ... (remaining 30707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 13653 34.83 - 69.66: 290 69.66 - 104.50: 40 104.50 - 139.33: 12 139.33 - 174.16: 17 Dihedral angle restraints: 14012 sinusoidal: 6308 harmonic: 7704 Sorted by residual: dihedral pdb=" CA TYR D 461 " pdb=" C TYR D 461 " pdb=" N ARG D 462 " pdb=" CA ARG D 462 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N ARG B 462 " pdb=" CA ARG B 462 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA TYR A 461 " pdb=" C TYR A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 14009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2483 0.035 - 0.071: 694 0.071 - 0.106: 160 0.106 - 0.142: 24 0.142 - 0.177: 11 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C2 POV C 904 " pdb=" C1 POV C 904 " pdb=" C3 POV C 904 " pdb=" O21 POV C 904 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" C2 POV C 902 " pdb=" C1 POV C 902 " pdb=" C3 POV C 902 " pdb=" O21 POV C 902 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C2 POV B 903 " pdb=" C1 POV B 903 " pdb=" C3 POV B 903 " pdb=" O21 POV B 903 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 3369 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 I8E B 906 " -0.012 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" C17 I8E B 906 " -0.017 2.00e-02 2.50e+03 pdb=" C3 I8E B 906 " 0.024 2.00e-02 2.50e+03 pdb=" C4 I8E B 906 " -0.016 2.00e-02 2.50e+03 pdb=" C5 I8E B 906 " -0.020 2.00e-02 2.50e+03 pdb=" C6 I8E B 906 " -0.013 2.00e-02 2.50e+03 pdb=" C7 I8E B 906 " -0.018 2.00e-02 2.50e+03 pdb=" C8 I8E B 906 " -0.019 2.00e-02 2.50e+03 pdb=" O15 I8E B 906 " 0.045 2.00e-02 2.50e+03 pdb=" O21 I8E B 906 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 I8E D 905 " 0.012 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" C17 I8E D 905 " 0.017 2.00e-02 2.50e+03 pdb=" C3 I8E D 905 " -0.023 2.00e-02 2.50e+03 pdb=" C4 I8E D 905 " 0.016 2.00e-02 2.50e+03 pdb=" C5 I8E D 905 " 0.020 2.00e-02 2.50e+03 pdb=" C6 I8E D 905 " 0.013 2.00e-02 2.50e+03 pdb=" C7 I8E D 905 " 0.018 2.00e-02 2.50e+03 pdb=" C8 I8E D 905 " 0.020 2.00e-02 2.50e+03 pdb=" O15 I8E D 905 " -0.045 2.00e-02 2.50e+03 pdb=" O21 I8E D 905 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 I8E C 905 " -0.012 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" C17 I8E C 905 " -0.017 2.00e-02 2.50e+03 pdb=" C3 I8E C 905 " 0.023 2.00e-02 2.50e+03 pdb=" C4 I8E C 905 " -0.016 2.00e-02 2.50e+03 pdb=" C5 I8E C 905 " -0.020 2.00e-02 2.50e+03 pdb=" C6 I8E C 905 " -0.013 2.00e-02 2.50e+03 pdb=" C7 I8E C 905 " -0.018 2.00e-02 2.50e+03 pdb=" C8 I8E C 905 " -0.020 2.00e-02 2.50e+03 pdb=" O15 I8E C 905 " 0.045 2.00e-02 2.50e+03 pdb=" O21 I8E C 905 " 0.047 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 209 2.58 - 3.16: 20293 3.16 - 3.74: 32289 3.74 - 4.32: 43520 4.32 - 4.90: 74451 Nonbonded interactions: 170762 Sorted by model distance: nonbonded pdb=" OG SER C 624 " pdb=" O13 POV C 904 " model vdw 2.001 3.040 nonbonded pdb=" OG SER B 624 " pdb=" O13 POV B 905 " model vdw 2.005 3.040 nonbonded pdb=" OG SER D 624 " pdb=" O13 POV D 904 " model vdw 2.009 3.040 nonbonded pdb=" OG SER A 444 " pdb=" O13 POV A 902 " model vdw 2.155 3.040 nonbonded pdb=" OG SER D 444 " pdb=" O13 POV D 903 " model vdw 2.161 3.040 ... (remaining 170757 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 59 through 903) selection = (chain 'B' and resid 59 through 903) selection = (chain 'C' and resid 59 through 903) selection = (chain 'D' and resid 59 through 903) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 20.070 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.004 0.062 22848 Z= 0.212 Angle : 0.629 5.344 30728 Z= 0.319 Chirality : 0.036 0.177 3372 Planarity : 0.004 0.082 3736 Dihedral : 16.488 174.158 8980 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 5.12 % Allowed : 9.47 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -1.18 (0.18), residues: 2596 helix: 0.88 (0.14), residues: 1552 sheet: -3.17 (0.59), residues: 64 loop : -3.52 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 693 TYR 0.013 0.001 TYR D 451 PHE 0.009 0.001 PHE B 316 TRP 0.003 0.001 TRP C 521 HIS 0.006 0.001 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00436 (22840) covalent geometry : angle 0.62829 (30712) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.12629 ( 16) hydrogen bonds : bond 0.15725 ( 1045) hydrogen bonds : angle 6.79987 ( 3039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 533 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 THR cc_start: 0.9010 (m) cc_final: 0.8779 (p) REVERT: A 347 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8026 (tt) REVERT: A 483 GLN cc_start: 0.7044 (tp40) cc_final: 0.6489 (tm-30) REVERT: A 485 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7653 (tm) REVERT: A 650 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5601 (m-10) REVERT: A 661 TYR cc_start: 0.8735 (t80) cc_final: 0.8337 (t80) REVERT: A 663 ILE cc_start: 0.9132 (tt) cc_final: 0.8914 (mt) REVERT: B 121 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8647 (mmmt) REVERT: B 336 THR cc_start: 0.9019 (m) cc_final: 0.8762 (p) REVERT: B 347 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 358 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8640 (tptt) REVERT: B 483 GLN cc_start: 0.6919 (tp40) cc_final: 0.6400 (tm-30) REVERT: B 485 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7660 (tm) REVERT: B 650 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5611 (m-10) REVERT: B 661 TYR cc_start: 0.8738 (t80) cc_final: 0.8359 (t80) REVERT: B 663 ILE cc_start: 0.9144 (tt) cc_final: 0.8897 (mt) REVERT: C 121 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8658 (mmmt) REVERT: C 336 THR cc_start: 0.9015 (m) cc_final: 0.8753 (p) REVERT: C 347 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7939 (tt) REVERT: C 358 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (tptt) REVERT: C 483 GLN cc_start: 0.7030 (tp40) cc_final: 0.6431 (tm-30) REVERT: C 485 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7645 (tm) REVERT: C 650 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: C 661 TYR cc_start: 0.8744 (t80) cc_final: 0.8354 (t80) REVERT: C 663 ILE cc_start: 0.9120 (tt) cc_final: 0.8875 (mt) REVERT: D 121 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8657 (mmmt) REVERT: D 336 THR cc_start: 0.9019 (m) cc_final: 0.8757 (p) REVERT: D 347 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7953 (tt) REVERT: D 358 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8642 (tptt) REVERT: D 483 GLN cc_start: 0.7032 (tp40) cc_final: 0.6420 (tm-30) REVERT: D 485 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7686 (tm) REVERT: D 650 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: D 661 TYR cc_start: 0.8760 (t80) cc_final: 0.8371 (t80) REVERT: D 663 ILE cc_start: 0.9153 (tt) cc_final: 0.8934 (mt) outliers start: 119 outliers final: 43 residues processed: 652 average time/residue: 0.1735 time to fit residues: 168.1848 Evaluate side-chains 371 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 258 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 227 GLN A 346 GLN A 417 HIS A 561 ASN B 71 ASN B 216 GLN B 227 GLN B 346 GLN B 417 HIS B 561 ASN C 71 ASN C 346 GLN C 417 HIS C 561 ASN D 71 ASN D 216 GLN D 227 GLN D 346 GLN D 417 HIS D 561 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130295 restraints weight = 29641.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134369 restraints weight = 21178.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136282 restraints weight = 16540.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137973 restraints weight = 14264.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140202 restraints weight = 12725.424| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22848 Z= 0.152 Angle : 0.754 11.528 30728 Z= 0.367 Chirality : 0.042 0.186 3372 Planarity : 0.005 0.081 3736 Dihedral : 18.837 179.361 3938 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 4.95 % Allowed : 16.14 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.82 (0.17), residues: 2596 helix: 0.98 (0.13), residues: 1580 sheet: -2.32 (0.64), residues: 40 loop : -3.20 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 462 TYR 0.019 0.001 TYR D 461 PHE 0.016 0.001 PHE C 316 TRP 0.007 0.001 TRP C 481 HIS 0.004 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00336 (22840) covalent geometry : angle 0.75338 (30712) SS BOND : bond 0.00743 ( 8) SS BOND : angle 1.15172 ( 16) hydrogen bonds : bond 0.04524 ( 1045) hydrogen bonds : angle 4.38098 ( 3039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 406 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8287 (mtpt) REVERT: A 166 ASP cc_start: 0.7875 (t70) cc_final: 0.7500 (t0) REVERT: A 281 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7770 (mm) REVERT: A 483 GLN cc_start: 0.7398 (tp40) cc_final: 0.6279 (tm-30) REVERT: A 541 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7718 (tp) REVERT: A 637 ILE cc_start: 0.5852 (pp) cc_final: 0.5432 (pt) REVERT: A 650 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5646 (m-10) REVERT: A 661 TYR cc_start: 0.8707 (t80) cc_final: 0.8252 (t80) REVERT: B 166 ASP cc_start: 0.7879 (t70) cc_final: 0.7575 (t0) REVERT: B 281 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7735 (mm) REVERT: B 322 ASP cc_start: 0.8078 (t70) cc_final: 0.7871 (t70) REVERT: B 358 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8859 (tttp) REVERT: B 483 GLN cc_start: 0.7334 (tp40) cc_final: 0.6267 (tm-30) REVERT: B 637 ILE cc_start: 0.5877 (pp) cc_final: 0.5476 (pt) REVERT: B 650 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.5693 (m-10) REVERT: B 661 TYR cc_start: 0.8727 (t80) cc_final: 0.8271 (t80) REVERT: C 166 ASP cc_start: 0.7900 (t70) cc_final: 0.7598 (t0) REVERT: C 281 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7731 (mm) REVERT: C 322 ASP cc_start: 0.8076 (t70) cc_final: 0.7865 (t70) REVERT: C 358 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8854 (tttp) REVERT: C 483 GLN cc_start: 0.7321 (tp40) cc_final: 0.6251 (tm-30) REVERT: C 637 ILE cc_start: 0.5879 (pp) cc_final: 0.5468 (pt) REVERT: C 650 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5721 (m-10) REVERT: C 661 TYR cc_start: 0.8716 (t80) cc_final: 0.8265 (t80) REVERT: D 121 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8526 (mmmt) REVERT: D 166 ASP cc_start: 0.7901 (t70) cc_final: 0.7537 (t0) REVERT: D 281 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7724 (mm) REVERT: D 358 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8860 (tttp) REVERT: D 429 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7823 (mp) REVERT: D 483 GLN cc_start: 0.7321 (tp40) cc_final: 0.6384 (tm-30) REVERT: D 637 ILE cc_start: 0.5868 (pp) cc_final: 0.5460 (pt) REVERT: D 650 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5710 (m-10) REVERT: D 661 TYR cc_start: 0.8725 (t80) cc_final: 0.8272 (t80) outliers start: 115 outliers final: 52 residues processed: 505 average time/residue: 0.1503 time to fit residues: 119.4878 Evaluate side-chains 399 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 334 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 161 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 160 HIS A 220 ASN A 274 GLN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 220 ASN B 274 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 274 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 242 ASN D 274 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122171 restraints weight = 30921.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126278 restraints weight = 22303.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128018 restraints weight = 17851.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128966 restraints weight = 15416.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130096 restraints weight = 14218.662| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 22848 Z= 0.240 Angle : 0.768 8.831 30728 Z= 0.377 Chirality : 0.044 0.178 3372 Planarity : 0.005 0.076 3736 Dihedral : 18.492 177.137 3908 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 7.31 % Allowed : 16.74 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.94 (0.17), residues: 2596 helix: 0.99 (0.13), residues: 1532 sheet: -2.02 (0.66), residues: 40 loop : -3.27 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 122 TYR 0.016 0.002 TYR D 451 PHE 0.020 0.002 PHE C 447 TRP 0.019 0.001 TRP A 493 HIS 0.006 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00581 (22840) covalent geometry : angle 0.76765 (30712) SS BOND : bond 0.00664 ( 8) SS BOND : angle 1.35298 ( 16) hydrogen bonds : bond 0.04848 ( 1045) hydrogen bonds : angle 4.43865 ( 3039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 341 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8253 (mtpt) REVERT: A 166 ASP cc_start: 0.7942 (t70) cc_final: 0.7618 (t0) REVERT: A 479 MET cc_start: 0.3471 (tpt) cc_final: 0.3012 (tpt) REVERT: A 483 GLN cc_start: 0.7259 (tp40) cc_final: 0.5882 (tm-30) REVERT: A 541 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7823 (tp) REVERT: A 637 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6063 (pt) REVERT: A 641 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7814 (p0) REVERT: A 650 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5741 (m-10) REVERT: B 121 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8152 (mtpt) REVERT: B 166 ASP cc_start: 0.7912 (t70) cc_final: 0.7564 (t0) REVERT: B 358 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8877 (tttp) REVERT: B 541 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7792 (tp) REVERT: B 637 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6048 (pt) REVERT: B 641 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7819 (p0) REVERT: B 650 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5694 (m-10) REVERT: B 725 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: C 166 ASP cc_start: 0.7980 (t70) cc_final: 0.7627 (t0) REVERT: C 358 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8891 (tttp) REVERT: C 541 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7807 (tp) REVERT: C 637 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.6061 (pt) REVERT: C 641 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7798 (p0) REVERT: C 650 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5686 (m-10) REVERT: D 121 LYS cc_start: 0.8722 (mmtp) cc_final: 0.8319 (mtpt) REVERT: D 358 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8876 (tttp) REVERT: D 429 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7885 (mp) REVERT: D 483 GLN cc_start: 0.7302 (tp40) cc_final: 0.6709 (tp40) REVERT: D 541 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7790 (tp) REVERT: D 637 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.6056 (pt) REVERT: D 641 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7826 (p0) REVERT: D 650 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5814 (m-10) REVERT: D 725 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7171 (pm20) outliers start: 170 outliers final: 93 residues processed: 469 average time/residue: 0.1475 time to fit residues: 109.5265 Evaluate side-chains 427 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 312 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 4 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 258 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 HIS C 160 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126740 restraints weight = 30558.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130695 restraints weight = 21809.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132412 restraints weight = 17409.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133614 restraints weight = 15211.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134526 restraints weight = 13927.309| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22848 Z= 0.142 Angle : 0.695 9.180 30728 Z= 0.343 Chirality : 0.041 0.160 3372 Planarity : 0.004 0.072 3736 Dihedral : 17.857 175.972 3908 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.52 % Favored : 88.33 % Rotamer: Outliers : 6.58 % Allowed : 18.12 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.83 (0.17), residues: 2596 helix: 1.07 (0.13), residues: 1536 sheet: -1.34 (0.70), residues: 40 loop : -3.24 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 122 TYR 0.012 0.001 TYR D 622 PHE 0.015 0.001 PHE A 447 TRP 0.026 0.001 TRP A 493 HIS 0.004 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00312 (22840) covalent geometry : angle 0.69436 (30712) SS BOND : bond 0.00438 ( 8) SS BOND : angle 1.45842 ( 16) hydrogen bonds : bond 0.04229 ( 1045) hydrogen bonds : angle 4.15873 ( 3039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 343 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8259 (mtpt) REVERT: A 166 ASP cc_start: 0.7903 (t70) cc_final: 0.7575 (t0) REVERT: A 479 MET cc_start: 0.3323 (tpt) cc_final: 0.2957 (tpt) REVERT: A 483 GLN cc_start: 0.7130 (tp40) cc_final: 0.5776 (tm-30) REVERT: A 635 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 637 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5656 (pt) REVERT: A 650 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: A 661 TYR cc_start: 0.8666 (t80) cc_final: 0.8333 (t80) REVERT: B 121 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8064 (mtmt) REVERT: B 166 ASP cc_start: 0.7890 (t70) cc_final: 0.7549 (t0) REVERT: B 358 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8851 (tttp) REVERT: B 541 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 635 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (tt) REVERT: B 637 ILE cc_start: 0.6097 (OUTLIER) cc_final: 0.5718 (pt) REVERT: B 650 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.5642 (m-10) REVERT: B 661 TYR cc_start: 0.8670 (t80) cc_final: 0.8340 (t80) REVERT: B 725 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: C 166 ASP cc_start: 0.7935 (t70) cc_final: 0.7587 (t0) REVERT: C 358 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8874 (tttp) REVERT: C 541 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7758 (tp) REVERT: C 635 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8650 (tt) REVERT: C 637 ILE cc_start: 0.6110 (OUTLIER) cc_final: 0.5724 (pt) REVERT: C 650 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5662 (m-10) REVERT: C 661 TYR cc_start: 0.8672 (t80) cc_final: 0.8350 (t80) REVERT: D 121 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8210 (mtpt) REVERT: D 166 ASP cc_start: 0.7919 (t70) cc_final: 0.7583 (t0) REVERT: D 358 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8774 (tptt) REVERT: D 429 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7832 (mp) REVERT: D 462 ARG cc_start: 0.6926 (mmt180) cc_final: 0.6297 (mmp80) REVERT: D 483 GLN cc_start: 0.7181 (tp40) cc_final: 0.6649 (tm-30) REVERT: D 541 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7764 (tp) REVERT: D 635 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8643 (tt) REVERT: D 637 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5716 (pt) REVERT: D 650 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.5744 (m-10) REVERT: D 661 TYR cc_start: 0.8674 (t80) cc_final: 0.8343 (t80) REVERT: D 725 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7084 (pm20) outliers start: 153 outliers final: 85 residues processed: 464 average time/residue: 0.1416 time to fit residues: 105.7110 Evaluate side-chains 415 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 309 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 16 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120463 restraints weight = 30691.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124097 restraints weight = 22723.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125920 restraints weight = 18551.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127422 restraints weight = 15952.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128495 restraints weight = 14382.533| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 22848 Z= 0.237 Angle : 0.769 9.495 30728 Z= 0.378 Chirality : 0.044 0.177 3372 Planarity : 0.005 0.071 3736 Dihedral : 17.331 164.514 3906 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.44 % Favored : 87.44 % Rotamer: Outliers : 7.44 % Allowed : 19.79 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.98 (0.17), residues: 2596 helix: 0.95 (0.14), residues: 1536 sheet: -1.60 (0.67), residues: 40 loop : -3.31 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 122 TYR 0.016 0.002 TYR B 540 PHE 0.025 0.002 PHE C 489 TRP 0.021 0.001 TRP D 493 HIS 0.004 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00569 (22840) covalent geometry : angle 0.76724 (30712) SS BOND : bond 0.00590 ( 8) SS BOND : angle 2.12124 ( 16) hydrogen bonds : bond 0.04772 ( 1045) hydrogen bonds : angle 4.30941 ( 3039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 307 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8274 (mtpt) REVERT: A 166 ASP cc_start: 0.7942 (t70) cc_final: 0.7643 (t0) REVERT: A 637 ILE cc_start: 0.6460 (OUTLIER) cc_final: 0.6088 (pt) REVERT: A 641 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7961 (p0) REVERT: A 650 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5664 (m-10) REVERT: B 121 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8102 (mtmt) REVERT: B 166 ASP cc_start: 0.7925 (t70) cc_final: 0.7601 (t0) REVERT: B 358 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8740 (tptt) REVERT: B 541 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7785 (tp) REVERT: B 578 MET cc_start: 0.8234 (mmp) cc_final: 0.7897 (mmp) REVERT: B 637 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.6151 (pt) REVERT: B 641 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7936 (p0) REVERT: B 650 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5690 (m-10) REVERT: B 725 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: C 121 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8129 (mtpt) REVERT: C 166 ASP cc_start: 0.7948 (t70) cc_final: 0.7617 (t0) REVERT: C 358 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8861 (tttp) REVERT: C 541 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 637 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6147 (pt) REVERT: C 641 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7909 (p0) REVERT: C 650 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5698 (m-10) REVERT: D 121 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8113 (mtpt) REVERT: D 358 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8746 (tptt) REVERT: D 429 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 483 GLN cc_start: 0.7324 (tp40) cc_final: 0.6853 (tp40) REVERT: D 541 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (tp) REVERT: D 637 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6162 (pt) REVERT: D 641 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7910 (p0) REVERT: D 650 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.5874 (m-10) REVERT: D 725 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7164 (pm20) outliers start: 173 outliers final: 108 residues processed: 452 average time/residue: 0.1485 time to fit residues: 107.4801 Evaluate side-chains 418 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 289 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 254 TYR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 159 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121405 restraints weight = 30883.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125147 restraints weight = 22333.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126839 restraints weight = 17903.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128292 restraints weight = 15581.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130064 restraints weight = 14077.746| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22848 Z= 0.213 Angle : 0.758 17.644 30728 Z= 0.370 Chirality : 0.043 0.171 3372 Planarity : 0.004 0.072 3736 Dihedral : 16.933 162.785 3906 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.02 % Favored : 86.86 % Rotamer: Outliers : 6.76 % Allowed : 21.00 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -1.03 (0.17), residues: 2596 helix: 0.91 (0.14), residues: 1536 sheet: -1.68 (0.69), residues: 40 loop : -3.32 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 122 TYR 0.014 0.002 TYR A 451 PHE 0.020 0.001 PHE B 316 TRP 0.022 0.001 TRP D 493 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00508 (22840) covalent geometry : angle 0.75599 (30712) SS BOND : bond 0.00762 ( 8) SS BOND : angle 2.22955 ( 16) hydrogen bonds : bond 0.04504 ( 1045) hydrogen bonds : angle 4.26086 ( 3039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 298 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8247 (mtpt) REVERT: A 166 ASP cc_start: 0.7929 (t70) cc_final: 0.7615 (t0) REVERT: A 637 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5985 (pt) REVERT: A 650 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5664 (m-10) REVERT: B 121 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8097 (mtmt) REVERT: B 166 ASP cc_start: 0.7933 (t70) cc_final: 0.7636 (t0) REVERT: B 358 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8744 (tptt) REVERT: B 541 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7749 (tp) REVERT: B 618 ASP cc_start: 0.5853 (OUTLIER) cc_final: 0.5227 (m-30) REVERT: B 637 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5967 (pt) REVERT: B 650 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5711 (m-10) REVERT: B 725 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: C 121 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8086 (mtpt) REVERT: C 166 ASP cc_start: 0.7941 (t70) cc_final: 0.7634 (t0) REVERT: C 358 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8742 (tptt) REVERT: C 541 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7752 (tp) REVERT: C 618 ASP cc_start: 0.5782 (OUTLIER) cc_final: 0.5181 (m-30) REVERT: C 637 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5968 (pt) REVERT: C 650 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5729 (m-10) REVERT: D 121 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8101 (mtpt) REVERT: D 358 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8752 (tptt) REVERT: D 429 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7838 (mp) REVERT: D 479 MET cc_start: 0.2426 (mtm) cc_final: 0.1346 (mmp) REVERT: D 483 GLN cc_start: 0.7305 (tp40) cc_final: 0.6305 (tm-30) REVERT: D 541 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7748 (tp) REVERT: D 618 ASP cc_start: 0.6183 (OUTLIER) cc_final: 0.4807 (m-30) REVERT: D 637 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5953 (pt) REVERT: D 650 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5852 (m-10) REVERT: D 725 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7139 (pm20) outliers start: 157 outliers final: 111 residues processed: 432 average time/residue: 0.1475 time to fit residues: 101.6040 Evaluate side-chains 414 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 283 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 254 TYR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 130 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 199 optimal weight: 0.4980 chunk 176 optimal weight: 0.5980 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126414 restraints weight = 30483.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130551 restraints weight = 21466.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132537 restraints weight = 17002.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134216 restraints weight = 14459.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135609 restraints weight = 12900.112| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22848 Z= 0.125 Angle : 0.697 9.609 30728 Z= 0.344 Chirality : 0.041 0.170 3372 Planarity : 0.004 0.072 3736 Dihedral : 16.412 164.134 3906 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.17 % Favored : 88.79 % Rotamer: Outliers : 5.46 % Allowed : 22.38 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.81 (0.17), residues: 2596 helix: 1.08 (0.14), residues: 1536 sheet: -1.46 (0.76), residues: 40 loop : -3.21 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 122 TYR 0.011 0.001 TYR D 622 PHE 0.016 0.001 PHE A 316 TRP 0.024 0.001 TRP D 493 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00272 (22840) covalent geometry : angle 0.69666 (30712) SS BOND : bond 0.00360 ( 8) SS BOND : angle 1.58914 ( 16) hydrogen bonds : bond 0.03894 ( 1045) hydrogen bonds : angle 4.00479 ( 3039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 328 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8094 (mtpt) REVERT: A 166 ASP cc_start: 0.7946 (t70) cc_final: 0.7648 (t0) REVERT: A 637 ILE cc_start: 0.5778 (pp) cc_final: 0.5399 (pt) REVERT: A 650 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5484 (m-10) REVERT: A 661 TYR cc_start: 0.8622 (t80) cc_final: 0.8309 (t80) REVERT: B 121 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8017 (mtpt) REVERT: B 166 ASP cc_start: 0.7944 (t70) cc_final: 0.7633 (t0) REVERT: B 358 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8691 (tptt) REVERT: B 637 ILE cc_start: 0.5848 (pp) cc_final: 0.5477 (pt) REVERT: B 650 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5558 (m-10) REVERT: B 661 TYR cc_start: 0.8621 (t80) cc_final: 0.8310 (t80) REVERT: C 121 LYS cc_start: 0.8620 (mmtm) cc_final: 0.7983 (mtpt) REVERT: C 166 ASP cc_start: 0.7956 (t70) cc_final: 0.7584 (t0) REVERT: C 358 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8694 (tptt) REVERT: C 637 ILE cc_start: 0.5857 (pp) cc_final: 0.5495 (pt) REVERT: C 650 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5548 (m-10) REVERT: C 661 TYR cc_start: 0.8631 (t80) cc_final: 0.8324 (t80) REVERT: D 358 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8682 (tptt) REVERT: D 429 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7728 (mp) REVERT: D 483 GLN cc_start: 0.7162 (tp40) cc_final: 0.6664 (tp40) REVERT: D 637 ILE cc_start: 0.5835 (pp) cc_final: 0.5472 (pt) REVERT: D 650 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5561 (m-10) REVERT: D 661 TYR cc_start: 0.8638 (t80) cc_final: 0.8325 (t80) REVERT: D 725 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7864 (pm20) outliers start: 127 outliers final: 88 residues processed: 425 average time/residue: 0.1391 time to fit residues: 95.2229 Evaluate side-chains 392 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 295 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 182 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 245 optimal weight: 0.1980 chunk 237 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 646 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 646 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.160280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120889 restraints weight = 30560.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123944 restraints weight = 22027.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125500 restraints weight = 17858.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127303 restraints weight = 15844.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128014 restraints weight = 14473.041| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22848 Z= 0.244 Angle : 0.775 16.608 30728 Z= 0.381 Chirality : 0.044 0.181 3372 Planarity : 0.005 0.070 3736 Dihedral : 16.368 160.178 3898 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.64 % Favored : 86.33 % Rotamer: Outliers : 5.94 % Allowed : 23.54 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -1.05 (0.17), residues: 2596 helix: 0.87 (0.14), residues: 1544 sheet: -1.68 (0.73), residues: 40 loop : -3.32 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 690 TYR 0.019 0.002 TYR D 540 PHE 0.034 0.002 PHE A 489 TRP 0.022 0.001 TRP D 493 HIS 0.010 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00587 (22840) covalent geometry : angle 0.77478 (30712) SS BOND : bond 0.00332 ( 8) SS BOND : angle 1.56460 ( 16) hydrogen bonds : bond 0.04606 ( 1045) hydrogen bonds : angle 4.25358 ( 3039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 282 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8179 (mtpt) REVERT: A 166 ASP cc_start: 0.7899 (t70) cc_final: 0.7611 (t0) REVERT: A 578 MET cc_start: 0.7985 (mmp) cc_final: 0.7592 (mmp) REVERT: A 586 ASP cc_start: 0.8814 (m-30) cc_final: 0.8498 (t0) REVERT: A 637 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6110 (pt) REVERT: A 650 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5611 (m-10) REVERT: A 690 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7255 (mtt180) REVERT: B 121 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8087 (mtmt) REVERT: B 166 ASP cc_start: 0.7897 (t70) cc_final: 0.7615 (t0) REVERT: B 358 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8739 (tptt) REVERT: B 637 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6097 (pt) REVERT: B 650 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5643 (m-10) REVERT: B 690 ARG cc_start: 0.7535 (mtp85) cc_final: 0.7213 (mtt180) REVERT: C 121 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8010 (mtpt) REVERT: C 167 THR cc_start: 0.8773 (p) cc_final: 0.8567 (t) REVERT: C 358 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8723 (tptt) REVERT: C 586 ASP cc_start: 0.8778 (m-30) cc_final: 0.8379 (t0) REVERT: C 637 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6113 (pt) REVERT: C 650 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5660 (m-10) REVERT: C 690 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7338 (mtt180) REVERT: D 122 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7271 (mtt90) REVERT: D 358 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8720 (tptt) REVERT: D 429 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7910 (mp) REVERT: D 586 ASP cc_start: 0.8765 (m-30) cc_final: 0.8371 (t0) REVERT: D 637 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6119 (pt) REVERT: D 650 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.5677 (m-10) REVERT: D 690 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7345 (mtt180) REVERT: D 725 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (pm20) outliers start: 138 outliers final: 96 residues processed: 396 average time/residue: 0.1487 time to fit residues: 95.2752 Evaluate side-chains 381 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 272 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 254 TYR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 132 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 745 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122698 restraints weight = 30700.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126653 restraints weight = 21932.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128332 restraints weight = 17487.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129533 restraints weight = 15251.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130575 restraints weight = 13840.407| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22848 Z= 0.172 Angle : 0.740 17.134 30728 Z= 0.361 Chirality : 0.042 0.174 3372 Planarity : 0.004 0.070 3736 Dihedral : 16.098 159.598 3898 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.79 % Favored : 87.13 % Rotamer: Outliers : 4.73 % Allowed : 24.74 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -1.01 (0.17), residues: 2596 helix: 0.94 (0.14), residues: 1544 sheet: -1.80 (0.74), residues: 40 loop : -3.36 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 690 TYR 0.011 0.001 TYR B 451 PHE 0.030 0.001 PHE A 489 TRP 0.027 0.001 TRP D 493 HIS 0.006 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00404 (22840) covalent geometry : angle 0.73965 (30712) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.47101 ( 16) hydrogen bonds : bond 0.04245 ( 1045) hydrogen bonds : angle 4.13096 ( 3039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 301 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8131 (mtpt) REVERT: A 135 LEU cc_start: 0.7894 (mm) cc_final: 0.7625 (mm) REVERT: A 166 ASP cc_start: 0.7889 (t70) cc_final: 0.7612 (t0) REVERT: A 578 MET cc_start: 0.7961 (mmp) cc_final: 0.7557 (mmp) REVERT: A 586 ASP cc_start: 0.8735 (m-30) cc_final: 0.8393 (t0) REVERT: A 637 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5882 (pt) REVERT: A 650 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5517 (m-10) REVERT: A 690 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7345 (mtt180) REVERT: B 121 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8059 (mtpt) REVERT: B 166 ASP cc_start: 0.7880 (t70) cc_final: 0.7605 (t0) REVERT: B 358 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8726 (tptt) REVERT: B 578 MET cc_start: 0.7593 (mmp) cc_final: 0.7367 (mmp) REVERT: B 637 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5856 (pt) REVERT: B 650 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5625 (m-10) REVERT: B 690 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7307 (mtt180) REVERT: C 121 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8061 (mtmt) REVERT: C 358 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8750 (tptt) REVERT: C 578 MET cc_start: 0.8079 (mmt) cc_final: 0.7761 (mmt) REVERT: C 586 ASP cc_start: 0.8749 (m-30) cc_final: 0.8365 (t0) REVERT: C 637 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5870 (pt) REVERT: C 650 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5644 (m-10) REVERT: C 690 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7409 (mtt180) REVERT: D 121 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8148 (mtpt) REVERT: D 135 LEU cc_start: 0.7655 (mm) cc_final: 0.7396 (mm) REVERT: D 358 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8733 (tptt) REVERT: D 429 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7812 (mp) REVERT: D 578 MET cc_start: 0.8066 (mmt) cc_final: 0.7742 (mmt) REVERT: D 586 ASP cc_start: 0.8734 (m-30) cc_final: 0.8343 (t0) REVERT: D 637 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5912 (pt) REVERT: D 650 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5640 (m-10) REVERT: D 690 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7364 (mtt180) REVERT: D 725 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7908 (pm20) outliers start: 110 outliers final: 82 residues processed: 392 average time/residue: 0.1542 time to fit residues: 96.2035 Evaluate side-chains 382 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 287 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 104 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 646 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121199 restraints weight = 30703.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124607 restraints weight = 22236.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126421 restraints weight = 17895.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127768 restraints weight = 15598.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128921 restraints weight = 14195.937| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22848 Z= 0.200 Angle : 0.773 17.582 30728 Z= 0.377 Chirality : 0.042 0.168 3372 Planarity : 0.004 0.069 3736 Dihedral : 15.990 156.487 3898 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.83 % Favored : 86.13 % Rotamer: Outliers : 4.99 % Allowed : 24.53 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -1.12 (0.17), residues: 2596 helix: 0.82 (0.14), residues: 1564 sheet: -1.91 (0.73), residues: 40 loop : -3.44 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 690 TYR 0.013 0.002 TYR B 451 PHE 0.028 0.001 PHE A 489 TRP 0.027 0.001 TRP D 493 HIS 0.005 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00475 (22840) covalent geometry : angle 0.77227 (30712) SS BOND : bond 0.00292 ( 8) SS BOND : angle 1.42963 ( 16) hydrogen bonds : bond 0.04442 ( 1045) hydrogen bonds : angle 4.18423 ( 3039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 282 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8123 (mtpt) REVERT: A 166 ASP cc_start: 0.7882 (t70) cc_final: 0.7597 (t0) REVERT: A 578 MET cc_start: 0.7976 (mmp) cc_final: 0.7501 (mmp) REVERT: A 586 ASP cc_start: 0.8713 (m-30) cc_final: 0.8390 (t0) REVERT: A 637 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.6046 (pt) REVERT: A 650 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5564 (m-10) REVERT: A 690 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7341 (mtt-85) REVERT: B 121 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8046 (mtpt) REVERT: B 166 ASP cc_start: 0.7880 (t70) cc_final: 0.7593 (t0) REVERT: B 358 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8753 (tptt) REVERT: B 578 MET cc_start: 0.7847 (mmp) cc_final: 0.7412 (mmp) REVERT: B 637 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6066 (pt) REVERT: B 650 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5640 (m-10) REVERT: C 121 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8074 (mtmt) REVERT: C 358 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (tptt) REVERT: C 586 ASP cc_start: 0.8689 (m-30) cc_final: 0.8317 (t0) REVERT: C 637 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6086 (pt) REVERT: C 650 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5638 (m-10) REVERT: C 690 ARG cc_start: 0.7687 (mtp85) cc_final: 0.7406 (mtt180) REVERT: D 122 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7431 (mtt90) REVERT: D 135 LEU cc_start: 0.7670 (mm) cc_final: 0.7400 (mm) REVERT: D 358 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8746 (tptt) REVERT: D 429 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 578 MET cc_start: 0.8089 (mmt) cc_final: 0.7845 (mmt) REVERT: D 586 ASP cc_start: 0.8678 (m-30) cc_final: 0.8297 (t0) REVERT: D 637 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6077 (pt) REVERT: D 650 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5643 (m-10) REVERT: D 690 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7405 (mtt180) outliers start: 116 outliers final: 90 residues processed: 386 average time/residue: 0.1544 time to fit residues: 95.5073 Evaluate side-chains 377 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 275 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 505 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 258 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 410 ASN B 646 GLN C 646 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126944 restraints weight = 30535.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130898 restraints weight = 21443.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132825 restraints weight = 16946.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134397 restraints weight = 14558.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135924 restraints weight = 13004.479| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22848 Z= 0.123 Angle : 0.719 17.353 30728 Z= 0.350 Chirality : 0.040 0.175 3372 Planarity : 0.004 0.071 3736 Dihedral : 15.477 157.177 3898 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.06 % Favored : 87.90 % Rotamer: Outliers : 3.74 % Allowed : 25.56 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.98 (0.17), residues: 2596 helix: 0.94 (0.14), residues: 1564 sheet: -1.60 (0.77), residues: 40 loop : -3.41 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 690 TYR 0.008 0.001 TYR B 451 PHE 0.029 0.001 PHE A 489 TRP 0.026 0.001 TRP D 493 HIS 0.006 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00265 (22840) covalent geometry : angle 0.71903 (30712) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.16948 ( 16) hydrogen bonds : bond 0.03754 ( 1045) hydrogen bonds : angle 3.95808 ( 3039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.52 seconds wall clock time: 67 minutes 14.63 seconds (4034.63 seconds total)