Starting phenix.real_space_refine on Wed May 21 21:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6l_42995/05_2025/8v6l_42995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6l_42995/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6l_42995/05_2025/8v6l_42995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6l_42995/05_2025/8v6l_42995.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6l_42995/05_2025/8v6l_42995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6l_42995/05_2025/8v6l_42995.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.62, per 1000 atoms: 0.61 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: 6.96 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.93 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: 6.65 Time building geometry restraints manager: 7.95 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 751 or resid 901 through 903)) selection = (chain 'B' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'C' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'D' and (resid 59 through 751 or resid 901 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 49.240 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.530 ------------------------------------------------------------------------------- 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 : 8.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP C 521 HIS 0.006 0.001 HIS C 471 PHE 0.009 0.001 PHE B 316 TYR 0.013 0.001 TYR D 451 ARG 0.003 0.000 ARG A 693 Details of bonding type rmsd hydrogen bonds : bond 0.15725 ( 1045) hydrogen bonds : angle 6.79987 ( 3039) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.12629 ( 16) covalent geometry : bond 0.00436 (22840) covalent geometry : angle 0.62829 (30712) *********************** 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 : 2.265 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: 0.3639 time to fit residues: 349.9118 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 : 2.224 ------------------------------------------------------------------------------- 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 219 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 274 GLN A 346 GLN B 71 ASN B 227 GLN B 274 GLN B 346 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 274 GLN C 346 GLN D 71 ASN D 227 GLN D 274 GLN D 346 GLN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120246 restraints weight = 30640.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124216 restraints weight = 22554.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125941 restraints weight = 18258.148| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22848 Z= 0.273 Angle : 0.833 9.969 30728 Z= 0.409 Chirality : 0.045 0.199 3372 Planarity : 0.005 0.076 3736 Dihedral : 19.099 179.523 3938 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.44 % Favored : 86.56 % Rotamer: Outliers : 6.50 % Allowed : 16.09 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2596 helix: 0.72 (0.13), residues: 1580 sheet: -2.61 (0.63), residues: 40 loop : -3.31 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 521 HIS 0.005 0.001 HIS C 256 PHE 0.022 0.002 PHE C 316 TYR 0.023 0.002 TYR D 461 ARG 0.005 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 1045) hydrogen bonds : angle 4.69012 ( 3039) SS BOND : bond 0.01021 ( 8) SS BOND : angle 1.32091 ( 16) covalent geometry : bond 0.00654 (22840) covalent geometry : angle 0.83298 (30712) *********************** 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 506 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 355 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8323 (mtpt) REVERT: A 166 ASP cc_start: 0.7936 (t70) cc_final: 0.7644 (t0) REVERT: A 255 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8322 (mt0) REVERT: A 429 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7961 (mp) REVERT: A 483 GLN cc_start: 0.7473 (tp40) cc_final: 0.6265 (tm-30) REVERT: A 641 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7759 (p0) REVERT: A 650 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5838 (m-10) REVERT: B 166 ASP cc_start: 0.7963 (t70) cc_final: 0.7662 (t0) REVERT: B 281 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 358 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8884 (tttp) REVERT: B 483 GLN cc_start: 0.7433 (tp40) cc_final: 0.6253 (tm-30) REVERT: B 619 CYS cc_start: 0.1007 (OUTLIER) cc_final: 0.0664 (t) REVERT: B 641 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7685 (p0) REVERT: B 650 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5846 (m-10) REVERT: C 166 ASP cc_start: 0.7954 (t70) cc_final: 0.7659 (t0) REVERT: C 358 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8898 (tttp) REVERT: C 483 GLN cc_start: 0.7434 (tp40) cc_final: 0.6243 (tm-30) REVERT: C 619 CYS cc_start: 0.1045 (OUTLIER) cc_final: 0.0717 (t) REVERT: C 641 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7741 (p0) REVERT: C 650 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5873 (m-10) REVERT: D 166 ASP cc_start: 0.7997 (t70) cc_final: 0.7609 (t0) REVERT: D 358 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8892 (tttp) REVERT: D 429 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 464 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7118 (mtm180) REVERT: D 483 GLN cc_start: 0.7426 (tp40) cc_final: 0.6247 (tm-30) REVERT: D 619 CYS cc_start: 0.0956 (OUTLIER) cc_final: 0.0632 (t) REVERT: D 641 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7646 (p0) REVERT: D 650 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5997 (m-10) outliers start: 151 outliers final: 91 residues processed: 484 average time/residue: 0.3239 time to fit residues: 246.6971 Evaluate side-chains 415 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 306 time to evaluate : 2.640 ------------------------------------------------------------------------------- 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 374 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE 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 508 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 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 ASP 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 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 281 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 408 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 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 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 619 CYS 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 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 732 LEU 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 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 453 ILE 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 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 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 619 CYS 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 694 LEU Chi-restraints excluded: chain C residue 732 LEU 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 358 LYS Chi-restraints excluded: chain D residue 374 SER 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 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU 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 548 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 619 CYS 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 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 88 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 417 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 160 HIS B 216 GLN B 417 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 160 HIS C 417 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 242 ASN D 417 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122833 restraints weight = 30799.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126954 restraints weight = 22079.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128715 restraints weight = 17547.387| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22848 Z= 0.200 Angle : 0.734 7.581 30728 Z= 0.364 Chirality : 0.042 0.168 3372 Planarity : 0.005 0.074 3736 Dihedral : 18.347 178.483 3916 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.02 % Favored : 87.83 % Rotamer: Outliers : 8.26 % Allowed : 17.69 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2596 helix: 0.87 (0.13), residues: 1532 sheet: -1.85 (0.68), residues: 40 loop : -3.40 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 521 HIS 0.004 0.001 HIS A 256 PHE 0.016 0.002 PHE C 316 TYR 0.014 0.002 TYR D 451 ARG 0.004 0.001 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 1045) hydrogen bonds : angle 4.45796 ( 3039) SS BOND : bond 0.01270 ( 8) SS BOND : angle 1.51568 ( 16) covalent geometry : bond 0.00472 (22840) covalent geometry : angle 0.73385 (30712) *********************** 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 532 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 340 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8268 (mtpt) REVERT: A 166 ASP cc_start: 0.7948 (t70) cc_final: 0.7624 (t0) REVERT: A 268 LEU cc_start: 0.9364 (tm) cc_final: 0.9126 (tt) REVERT: A 429 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7850 (mp) REVERT: A 479 MET cc_start: 0.3503 (tpt) cc_final: 0.3156 (tpt) REVERT: A 483 GLN cc_start: 0.7256 (tp40) cc_final: 0.5878 (tm-30) REVERT: A 541 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7877 (tp) REVERT: A 578 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8060 (mmp) REVERT: A 637 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.5964 (pt) REVERT: A 641 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7959 (p0) REVERT: A 650 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5671 (m-10) REVERT: B 121 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8170 (mtpt) REVERT: B 166 ASP cc_start: 0.7969 (t70) cc_final: 0.7606 (t0) REVERT: B 268 LEU cc_start: 0.9360 (tm) cc_final: 0.9131 (tt) REVERT: B 358 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8762 (tptt) REVERT: B 541 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7865 (tp) REVERT: B 578 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7799 (mmp) REVERT: B 637 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.5974 (pt) REVERT: B 641 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7904 (p0) REVERT: B 650 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5783 (m-10) REVERT: B 725 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: B 749 LEU cc_start: 0.8254 (tp) cc_final: 0.8045 (tt) REVERT: C 166 ASP cc_start: 0.7981 (t70) cc_final: 0.7615 (t0) REVERT: C 268 LEU cc_start: 0.9364 (tm) cc_final: 0.9125 (tt) REVERT: C 358 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8779 (tptt) REVERT: C 541 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7880 (tp) REVERT: C 578 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8021 (mmp) REVERT: C 637 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.5946 (pt) REVERT: C 641 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7871 (p0) REVERT: C 650 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5800 (m-10) REVERT: D 268 LEU cc_start: 0.9371 (tm) cc_final: 0.9130 (tt) REVERT: D 358 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8775 (tptt) REVERT: D 429 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7917 (mp) REVERT: D 541 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7875 (tp) REVERT: D 578 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7994 (mmp) REVERT: D 637 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.5938 (pt) REVERT: D 641 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7898 (p0) REVERT: D 650 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5803 (m-10) REVERT: D 725 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7121 (pm20) outliers start: 192 outliers final: 104 residues processed: 491 average time/residue: 0.3137 time to fit residues: 243.8189 Evaluate side-chains 433 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 302 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG 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 508 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 557 LEU Chi-restraints excluded: chain A residue 578 MET 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 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 358 LYS Chi-restraints excluded: chain B residue 374 SER 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 453 ILE 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 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 578 MET 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 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 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE 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 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 578 MET 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 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 286 GLN 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 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG 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 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 578 MET Chi-restraints excluded: chain D residue 591 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 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 183 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 197 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- 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 561 ASN B 242 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 242 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 HIS D 561 ASN D 745 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119429 restraints weight = 31281.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123427 restraints weight = 22892.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125391 restraints weight = 18391.297| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3248 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= 0.256 Angle : 0.777 7.913 30728 Z= 0.384 Chirality : 0.044 0.181 3372 Planarity : 0.005 0.073 3736 Dihedral : 17.975 173.953 3916 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.14 % Favored : 86.71 % Rotamer: Outliers : 7.96 % Allowed : 19.19 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2596 helix: 0.81 (0.13), residues: 1536 sheet: -1.85 (0.65), residues: 40 loop : -3.45 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 493 HIS 0.005 0.001 HIS C 256 PHE 0.020 0.002 PHE D 316 TYR 0.015 0.002 TYR D 451 ARG 0.004 0.001 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 1045) hydrogen bonds : angle 4.48324 ( 3039) SS BOND : bond 0.00784 ( 8) SS BOND : angle 1.40081 ( 16) covalent geometry : bond 0.00614 (22840) covalent geometry : angle 0.77680 (30712) *********************** 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 497 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 312 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8291 (mtpt) REVERT: A 166 ASP cc_start: 0.7963 (t70) cc_final: 0.7655 (t0) REVERT: A 268 LEU cc_start: 0.9343 (tm) cc_final: 0.9088 (tt) REVERT: A 429 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 541 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7819 (tp) REVERT: A 637 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.6040 (pt) REVERT: A 641 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7956 (p0) REVERT: A 650 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5730 (m-10) REVERT: B 121 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8209 (mtmt) REVERT: B 166 ASP cc_start: 0.7967 (t70) cc_final: 0.7623 (t0) REVERT: B 358 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8757 (tptt) REVERT: B 541 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7854 (tp) REVERT: B 637 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6060 (pt) REVERT: B 641 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7918 (p0) REVERT: B 650 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.5872 (m-10) REVERT: B 725 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: B 749 LEU cc_start: 0.8275 (tp) cc_final: 0.8015 (tt) REVERT: C 121 LYS cc_start: 0.8708 (mmtm) cc_final: 0.8133 (mtpt) REVERT: C 166 ASP cc_start: 0.7982 (t70) cc_final: 0.7655 (t0) REVERT: C 268 LEU cc_start: 0.9343 (tm) cc_final: 0.9089 (tt) REVERT: C 358 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8906 (tttp) REVERT: C 541 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7842 (tp) REVERT: C 637 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6076 (pt) REVERT: C 641 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7858 (p0) REVERT: C 650 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: D 358 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8769 (tptt) REVERT: D 429 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7966 (mp) REVERT: D 541 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7849 (tp) REVERT: D 637 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6074 (pt) REVERT: D 641 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7899 (p0) REVERT: D 650 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5950 (m-10) REVERT: D 725 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7224 (pm20) outliers start: 185 outliers final: 127 residues processed: 464 average time/residue: 0.2990 time to fit residues: 221.8730 Evaluate side-chains 445 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 295 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 374 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE 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 485 LEU Chi-restraints excluded: chain A residue 491 LEU 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 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 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 644 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 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 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE 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 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 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 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 641 ASP Chi-restraints excluded: chain B residue 644 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 732 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 746 VAL 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 402 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE 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 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 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 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 641 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 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 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 374 SER 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 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU 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 578 MET 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 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 732 LEU 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 183 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 236 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125835 restraints weight = 30682.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129779 restraints weight = 21544.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131619 restraints weight = 17172.035| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22848 Z= 0.126 Angle : 0.692 17.351 30728 Z= 0.340 Chirality : 0.041 0.160 3372 Planarity : 0.004 0.074 3736 Dihedral : 17.059 165.058 3916 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.63 % Favored : 88.21 % Rotamer: Outliers : 6.37 % Allowed : 21.77 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2596 helix: 1.04 (0.14), residues: 1536 sheet: -1.32 (0.73), residues: 40 loop : -3.42 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 493 HIS 0.004 0.001 HIS A 256 PHE 0.015 0.001 PHE D 316 TYR 0.010 0.001 TYR D 622 ARG 0.005 0.000 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 1045) hydrogen bonds : angle 4.12450 ( 3039) SS BOND : bond 0.00146 ( 8) SS BOND : angle 1.53221 ( 16) covalent geometry : bond 0.00273 (22840) covalent geometry : angle 0.69127 (30712) *********************** 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 505 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 357 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8261 (mtpt) REVERT: A 166 ASP cc_start: 0.7949 (t70) cc_final: 0.7643 (t0) REVERT: A 268 LEU cc_start: 0.9252 (tm) cc_final: 0.9021 (tt) REVERT: A 429 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 541 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7772 (tp) REVERT: A 637 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5430 (pt) REVERT: A 650 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5650 (m-10) REVERT: A 661 TYR cc_start: 0.8617 (t80) cc_final: 0.8242 (t80) REVERT: B 121 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8088 (mtmt) REVERT: B 166 ASP cc_start: 0.7951 (t70) cc_final: 0.7605 (t0) REVERT: B 268 LEU cc_start: 0.9269 (tm) cc_final: 0.9046 (tt) REVERT: B 358 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8734 (tptt) REVERT: B 541 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 637 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5504 (pt) REVERT: B 650 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5737 (m-10) REVERT: B 661 TYR cc_start: 0.8616 (t80) cc_final: 0.8249 (t80) REVERT: B 725 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: B 749 LEU cc_start: 0.8138 (tp) cc_final: 0.7915 (tt) REVERT: C 121 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8046 (mtpt) REVERT: C 166 ASP cc_start: 0.7953 (t70) cc_final: 0.7595 (t0) REVERT: C 268 LEU cc_start: 0.9259 (tm) cc_final: 0.9035 (tt) REVERT: C 358 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8751 (tptt) REVERT: C 541 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7801 (tp) REVERT: C 637 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5500 (pt) REVERT: C 650 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5600 (m-10) REVERT: C 661 TYR cc_start: 0.8618 (t80) cc_final: 0.8252 (t80) REVERT: D 121 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8098 (mtpt) REVERT: D 268 LEU cc_start: 0.9268 (tm) cc_final: 0.9043 (tt) REVERT: D 358 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8722 (tptt) REVERT: D 429 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7771 (mp) REVERT: D 541 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7778 (tp) REVERT: D 637 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5502 (pt) REVERT: D 650 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5772 (m-10) REVERT: D 661 TYR cc_start: 0.8627 (t80) cc_final: 0.8245 (t80) REVERT: D 725 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7143 (pm20) outliers start: 148 outliers final: 91 residues processed: 471 average time/residue: 0.3116 time to fit residues: 233.9365 Evaluate side-chains 422 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 312 time to evaluate : 2.320 ------------------------------------------------------------------------------- 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 414 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE 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 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 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 414 ASP Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE 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 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 608 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 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 414 ASP Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE 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 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 608 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 668 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 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU 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 608 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 44 optimal weight: 0.0870 chunk 139 optimal weight: 9.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.167823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127912 restraints weight = 30303.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131943 restraints weight = 21369.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133932 restraints weight = 16802.665| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- 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: 16 | |-----------------------------------------------------------------------------| |-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: 16 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22848 Z= 0.118 Angle : 0.685 8.813 30728 Z= 0.339 Chirality : 0.040 0.169 3372 Planarity : 0.004 0.072 3736 Dihedral : 16.388 165.534 3916 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 6.11 % Allowed : 22.68 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2596 helix: 1.10 (0.13), residues: 1536 sheet: -1.17 (0.79), residues: 40 loop : -3.37 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 493 HIS 0.004 0.001 HIS A 256 PHE 0.015 0.001 PHE D 316 TYR 0.016 0.001 TYR D 540 ARG 0.005 0.000 ARG A 690 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1045) hydrogen bonds : angle 3.97754 ( 3039) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.88014 ( 16) covalent geometry : bond 0.00250 (22840) covalent geometry : angle 0.68395 (30712) *********************** 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 492 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 350 time to evaluate : 2.238 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: 0.8886 (mmmt) cc_final: 0.8195 (mtpt) REVERT: A 166 ASP cc_start: 0.7929 (t70) cc_final: 0.7629 (t0) REVERT: A 429 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7723 (mp) REVERT: A 586 ASP cc_start: 0.8780 (m-30) cc_final: 0.8475 (t0) REVERT: A 637 ILE cc_start: 0.5520 (pp) cc_final: 0.5119 (pt) REVERT: A 650 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.5478 (m-10) REVERT: A 661 TYR cc_start: 0.8608 (t80) cc_final: 0.8250 (t80) REVERT: A 717 MET cc_start: 0.7572 (mtp) cc_final: 0.7309 (mtt) REVERT: B 121 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8079 (mtpt) REVERT: B 166 ASP cc_start: 0.7935 (t70) cc_final: 0.7574 (t0) REVERT: B 358 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8747 (tptt) REVERT: B 618 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.5094 (m-30) REVERT: B 637 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.5162 (pt) REVERT: B 650 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5517 (m-10) REVERT: B 661 TYR cc_start: 0.8610 (t80) cc_final: 0.8243 (t80) REVERT: B 749 LEU cc_start: 0.8106 (tp) cc_final: 0.7906 (tt) REVERT: C 121 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8080 (mtmt) REVERT: C 358 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8848 (tttp) REVERT: C 618 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.4538 (m-30) REVERT: C 637 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5156 (pt) REVERT: C 650 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5616 (m-10) REVERT: C 657 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7845 (mp) REVERT: C 661 TYR cc_start: 0.8607 (t80) cc_final: 0.8232 (t80) REVERT: D 121 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8088 (mtmt) REVERT: D 358 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8747 (tptt) REVERT: D 429 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7717 (mp) REVERT: D 618 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.4729 (m-30) REVERT: D 637 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5146 (pt) REVERT: D 650 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5559 (m-10) REVERT: D 661 TYR cc_start: 0.8613 (t80) cc_final: 0.8240 (t80) outliers start: 142 outliers final: 98 residues processed: 467 average time/residue: 0.2950 time to fit residues: 219.8285 Evaluate side-chains 416 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 302 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 414 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 LEU 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 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 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 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 414 ASP Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE 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 497 ILE 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 608 LEU 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 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 210 GLU 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 414 ASP Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE 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 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 608 LEU 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 668 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 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 414 ASP Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 508 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 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 694 LEU Chi-restraints excluded: chain D residue 723 VAL 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 192 optimal weight: 0.0570 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 646 GLN C 745 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 646 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129572 restraints weight = 30649.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133641 restraints weight = 21531.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135508 restraints weight = 16941.988| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22848 Z= 0.117 Angle : 0.681 8.542 30728 Z= 0.337 Chirality : 0.040 0.167 3372 Planarity : 0.004 0.071 3736 Dihedral : 15.765 166.068 3906 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 5.59 % Allowed : 22.93 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2596 helix: 1.16 (0.14), residues: 1544 sheet: -1.04 (0.80), residues: 40 loop : -3.36 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 493 HIS 0.012 0.001 HIS C 585 PHE 0.015 0.001 PHE D 316 TYR 0.010 0.001 TYR D 622 ARG 0.003 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1045) hydrogen bonds : angle 3.94235 ( 3039) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.41175 ( 16) covalent geometry : bond 0.00246 (22840) covalent geometry : angle 0.68031 (30712) *********************** 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 457 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 327 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8156 (mtpt) REVERT: A 166 ASP cc_start: 0.7906 (t70) cc_final: 0.7623 (t0) REVERT: A 586 ASP cc_start: 0.8793 (m-30) cc_final: 0.8393 (t0) REVERT: A 618 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.4146 (m-30) REVERT: A 637 ILE cc_start: 0.5495 (pp) cc_final: 0.5063 (pt) REVERT: A 650 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.5369 (m-10) REVERT: A 657 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 661 TYR cc_start: 0.8584 (t80) cc_final: 0.8218 (t80) REVERT: B 121 LYS cc_start: 0.8762 (mmmt) cc_final: 0.7986 (mtpt) REVERT: B 358 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8674 (tptt) REVERT: B 637 ILE cc_start: 0.5494 (pp) cc_final: 0.5065 (pt) REVERT: B 650 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.5450 (m-10) REVERT: B 657 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 661 TYR cc_start: 0.8572 (t80) cc_final: 0.8195 (t80) REVERT: C 358 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8681 (tptt) REVERT: C 637 ILE cc_start: 0.5487 (pp) cc_final: 0.5054 (pt) REVERT: C 650 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.5543 (m-10) REVERT: C 657 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7898 (mp) REVERT: C 661 TYR cc_start: 0.8574 (t80) cc_final: 0.8205 (t80) REVERT: D 358 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8664 (tptt) REVERT: D 637 ILE cc_start: 0.5489 (pp) cc_final: 0.5061 (pt) REVERT: D 650 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.5521 (m-10) REVERT: D 657 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7812 (mp) REVERT: D 661 TYR cc_start: 0.8576 (t80) cc_final: 0.8204 (t80) outliers start: 130 outliers final: 96 residues processed: 433 average time/residue: 0.2937 time to fit residues: 206.3680 Evaluate side-chains 408 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 300 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 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 414 ASP Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 485 LEU 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 508 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 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 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 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 414 ASP Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE 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 497 ILE 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 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 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 402 SER Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL 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 508 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 588 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 668 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 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 414 ASP Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 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 588 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 723 VAL 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 204 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 8 optimal weight: 0.2980 chunk 170 optimal weight: 1.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 HIS C 242 ASN C 410 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121222 restraints weight = 30775.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124422 restraints weight = 22254.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126369 restraints weight = 18183.032| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22848 Z= 0.240 Angle : 0.792 15.630 30728 Z= 0.390 Chirality : 0.044 0.221 3372 Planarity : 0.005 0.068 3736 Dihedral : 15.816 161.254 3898 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 5.81 % Allowed : 23.54 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2596 helix: 1.01 (0.14), residues: 1540 sheet: -2.68 (0.63), residues: 64 loop : -3.35 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 493 HIS 0.007 0.001 HIS A 417 PHE 0.023 0.002 PHE B 316 TYR 0.021 0.002 TYR B 540 ARG 0.010 0.001 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1045) hydrogen bonds : angle 4.17613 ( 3039) SS BOND : bond 0.00409 ( 8) SS BOND : angle 1.64155 ( 16) covalent geometry : bond 0.00571 (22840) covalent geometry : angle 0.79125 (30712) *********************** 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 424 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 289 time to evaluate : 2.429 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8173 (mtpt) REVERT: A 166 ASP cc_start: 0.7899 (t70) cc_final: 0.7600 (t0) REVERT: A 429 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7780 (mp) REVERT: A 578 MET cc_start: 0.7691 (mmp) cc_final: 0.7480 (mmp) REVERT: A 618 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.4197 (m-30) REVERT: A 637 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6079 (pt) REVERT: A 650 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.5484 (m-10) REVERT: A 690 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7319 (mtt180) REVERT: B 121 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8018 (mtpt) REVERT: B 358 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8714 (tptt) REVERT: B 618 ASP cc_start: 0.5746 (OUTLIER) cc_final: 0.4562 (m-30) REVERT: B 637 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6074 (pt) REVERT: B 650 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: B 690 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7259 (mtt180) REVERT: C 637 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6078 (pt) REVERT: C 650 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.5593 (m-10) REVERT: C 690 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7251 (mtt180) REVERT: D 358 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8710 (tptt) REVERT: D 429 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7791 (mp) REVERT: D 637 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.6072 (pt) REVERT: D 650 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5697 (m-10) REVERT: D 690 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7318 (mtt180) outliers start: 135 outliers final: 95 residues processed: 401 average time/residue: 0.3038 time to fit residues: 195.1181 Evaluate side-chains 392 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 283 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 VAL 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 608 LEU 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 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 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 430 HIS Chi-restraints excluded: chain B residue 453 ILE 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 497 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 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 653 LEU 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 316 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 357 LEU 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 458 VAL 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 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 668 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 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 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 534 ILE 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 653 LEU 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 723 VAL 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 114 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 646 GLN D 410 ASN ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127022 restraints weight = 30418.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130959 restraints weight = 21674.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132698 restraints weight = 17240.997| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4122 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= 0.129 Angle : 0.720 16.229 30728 Z= 0.351 Chirality : 0.041 0.221 3372 Planarity : 0.004 0.070 3736 Dihedral : 15.439 162.494 3894 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.94 % Favored : 88.02 % Rotamer: Outliers : 4.91 % Allowed : 24.35 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2596 helix: 1.17 (0.14), residues: 1540 sheet: -1.46 (0.78), residues: 40 loop : -3.46 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 493 HIS 0.004 0.001 HIS D 417 PHE 0.018 0.001 PHE C 316 TYR 0.009 0.001 TYR D 451 ARG 0.007 0.000 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1045) hydrogen bonds : angle 3.97708 ( 3039) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.17414 ( 16) covalent geometry : bond 0.00287 (22840) covalent geometry : angle 0.71996 (30712) *********************** 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 419 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 305 time to evaluate : 2.421 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8080 (mtpt) REVERT: A 166 ASP cc_start: 0.7993 (t70) cc_final: 0.7639 (t0) REVERT: A 493 TRP cc_start: 0.8106 (t-100) cc_final: 0.7782 (t-100) REVERT: A 578 MET cc_start: 0.7650 (mmp) cc_final: 0.7360 (mmp) REVERT: A 618 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.4284 (m-30) REVERT: A 637 ILE cc_start: 0.5676 (OUTLIER) cc_final: 0.5290 (pt) REVERT: A 650 TYR cc_start: 0.6147 (OUTLIER) cc_final: 0.5480 (m-10) REVERT: A 661 TYR cc_start: 0.8669 (t80) cc_final: 0.8255 (t80) REVERT: A 690 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7373 (mtt180) REVERT: B 121 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8031 (mtpt) REVERT: B 358 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (tptt) REVERT: B 493 TRP cc_start: 0.8104 (t-100) cc_final: 0.7755 (t-100) REVERT: B 578 MET cc_start: 0.7551 (mmp) cc_final: 0.7267 (mmp) REVERT: B 637 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5446 (pt) REVERT: B 650 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5565 (m-10) REVERT: B 661 TYR cc_start: 0.8644 (t80) cc_final: 0.8233 (t80) REVERT: B 690 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7336 (mtt180) REVERT: C 493 TRP cc_start: 0.8095 (t-100) cc_final: 0.7748 (t-100) REVERT: C 578 MET cc_start: 0.7533 (mmp) cc_final: 0.7239 (mmp) REVERT: C 637 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5439 (pt) REVERT: C 650 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5502 (m-10) REVERT: C 661 TYR cc_start: 0.8652 (t80) cc_final: 0.8228 (t80) REVERT: C 690 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7380 (mtt180) REVERT: D 358 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8657 (tptt) REVERT: D 493 TRP cc_start: 0.8079 (t-100) cc_final: 0.7743 (t-100) REVERT: D 578 MET cc_start: 0.7536 (mmp) cc_final: 0.7239 (mmp) REVERT: D 637 ILE cc_start: 0.5613 (OUTLIER) cc_final: 0.5213 (pt) REVERT: D 650 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5525 (m-10) REVERT: D 661 TYR cc_start: 0.8660 (t80) cc_final: 0.8230 (t80) REVERT: D 690 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7382 (mtt180) outliers start: 114 outliers final: 88 residues processed: 404 average time/residue: 0.2925 time to fit residues: 190.4529 Evaluate side-chains 385 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 286 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 485 LEU 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 553 LEU Chi-restraints excluded: chain A residue 557 LEU 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 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 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 430 HIS Chi-restraints excluded: chain B residue 453 ILE 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 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 720 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 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL 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 553 LEU Chi-restraints excluded: chain C residue 557 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 668 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 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 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 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 694 LEU Chi-restraints excluded: chain D residue 720 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 3 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 585 HIS ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 274 GLN C 585 HIS C 646 GLN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124291 restraints weight = 30687.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127922 restraints weight = 21665.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129981 restraints weight = 17207.877| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 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 = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4174 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= 0.155 Angle : 0.729 16.160 30728 Z= 0.355 Chirality : 0.042 0.210 3372 Planarity : 0.004 0.069 3736 Dihedral : 15.192 160.118 3894 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 4.73 % Allowed : 24.44 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2596 helix: 1.07 (0.14), residues: 1568 sheet: -1.51 (0.78), residues: 40 loop : -3.57 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 493 HIS 0.005 0.001 HIS D 417 PHE 0.019 0.001 PHE B 316 TYR 0.010 0.001 TYR B 451 ARG 0.007 0.000 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 1045) hydrogen bonds : angle 3.98349 ( 3039) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.18027 ( 16) covalent geometry : bond 0.00358 (22840) covalent geometry : angle 0.72918 (30712) ********************** 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 399 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 289 time to evaluate : 2.245 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8066 (mtpt) REVERT: A 493 TRP cc_start: 0.8137 (t-100) cc_final: 0.7843 (t-100) REVERT: A 618 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.4187 (m-30) REVERT: A 637 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5552 (pt) REVERT: A 650 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5466 (m-10) REVERT: A 690 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7376 (mtt180) REVERT: B 358 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8707 (tptt) REVERT: B 493 TRP cc_start: 0.8126 (t-100) cc_final: 0.7814 (t-100) REVERT: B 637 ILE cc_start: 0.5932 (OUTLIER) cc_final: 0.5549 (pt) REVERT: B 650 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5597 (m-10) REVERT: B 690 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7329 (mtt-85) REVERT: C 637 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5544 (pt) REVERT: C 650 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5405 (m-10) REVERT: C 690 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7343 (mtt-85) REVERT: D 493 TRP cc_start: 0.8119 (t-100) cc_final: 0.7814 (t-100) REVERT: D 637 ILE cc_start: 0.5900 (OUTLIER) cc_final: 0.5530 (pt) REVERT: D 650 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.5450 (m-10) REVERT: D 690 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7353 (mtt180) outliers start: 110 outliers final: 89 residues processed: 383 average time/residue: 0.2957 time to fit residues: 181.8265 Evaluate side-chains 380 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 281 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 357 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 457 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 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 608 LEU 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 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 430 HIS Chi-restraints excluded: chain B residue 453 ILE 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 497 ILE 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 154 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 343 THR 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 458 VAL 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 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 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 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 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 398 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE 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 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 653 LEU 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: 4.9990 chunk 233 optimal weight: 30.0000 chunk 126 optimal weight: 0.5980 chunk 226 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 646 GLN ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126843 restraints weight = 30443.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130917 restraints weight = 21795.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132630 restraints weight = 17196.764| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22848 Z= 0.138 Angle : 0.719 16.384 30728 Z= 0.350 Chirality : 0.041 0.209 3372 Planarity : 0.004 0.069 3736 Dihedral : 14.900 159.396 3890 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 4.69 % Allowed : 24.40 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2596 helix: 1.11 (0.14), residues: 1568 sheet: -1.55 (0.79), residues: 40 loop : -3.58 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 493 HIS 0.005 0.001 HIS A 417 PHE 0.020 0.001 PHE B 316 TYR 0.009 0.001 TYR B 451 ARG 0.007 0.000 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1045) hydrogen bonds : angle 3.93800 ( 3039) SS BOND : bond 0.00217 ( 8) SS BOND : angle 1.04383 ( 16) covalent geometry : bond 0.00313 (22840) covalent geometry : angle 0.71878 (30712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7143.05 seconds wall clock time: 125 minutes 56.81 seconds (7556.81 seconds total)