Starting phenix.real_space_refine on Thu Aug 8 04:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/08_2024/8v6l_42995.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/08_2024/8v6l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/08_2024/8v6l_42995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/08_2024/8v6l_42995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/08_2024/8v6l_42995.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/08_2024/8v6l_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 Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.26, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 7.94 Conformation dependent library (CDL) restraints added in 3.4 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: 5.90 Time building geometry restraints manager: 8.72 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: 97.67 - 104.94: 288 104.94 - 112.21: 11288 112.21 - 119.48: 7997 119.48 - 126.75: 10836 126.75 - 134.01: 303 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: 0.900 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: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.180 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.080 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:2.540 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.100 ------------------------------------------------------------------------------- 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 22840 Z= 0.282 Angle : 0.628 5.344 30712 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 *********************** 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 fitting. rotamer outliers: 119 poor density : 533 time to evaluate : 2.452 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: 0.3738 time to fit residues: 360.2362 Evaluate side-chains 371 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 313 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 22840 Z= 0.419 Angle : 0.833 9.969 30712 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 *********************** 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 fitting. rotamer outliers: 151 poor density : 355 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8323 (mtpt) REVERT: A 166 ASP cc_start: 0.7964 (t70) cc_final: 0.7652 (t0) REVERT: A 255 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8289 (mt0) REVERT: A 429 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 483 GLN cc_start: 0.7491 (tp40) cc_final: 0.6399 (tm-30) REVERT: A 641 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7657 (p0) REVERT: A 650 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5773 (m-10) REVERT: B 166 ASP cc_start: 0.8100 (t70) cc_final: 0.7760 (t0) REVERT: B 281 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7831 (mm) REVERT: B 322 ASP cc_start: 0.8367 (t70) cc_final: 0.8159 (t70) REVERT: B 336 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8673 (p) REVERT: B 358 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8822 (tttp) REVERT: B 483 GLN cc_start: 0.7479 (tp40) cc_final: 0.6306 (tm-30) REVERT: B 619 CYS cc_start: 0.0994 (OUTLIER) cc_final: 0.0625 (t) REVERT: B 641 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7564 (p0) REVERT: B 650 TYR cc_start: 0.6330 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: C 166 ASP cc_start: 0.8110 (t70) cc_final: 0.7770 (t0) REVERT: C 322 ASP cc_start: 0.8361 (t70) cc_final: 0.8146 (t70) REVERT: C 358 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8826 (tttp) REVERT: C 483 GLN cc_start: 0.7463 (tp40) cc_final: 0.6310 (tm-30) REVERT: C 619 CYS cc_start: 0.1044 (OUTLIER) cc_final: 0.0703 (t) REVERT: C 641 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7607 (p0) REVERT: C 650 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5808 (m-10) REVERT: D 166 ASP cc_start: 0.8126 (t70) cc_final: 0.7681 (t0) REVERT: D 358 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8826 (tttp) REVERT: D 429 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7760 (mp) REVERT: D 483 GLN cc_start: 0.7475 (tp40) cc_final: 0.6306 (tm-30) REVERT: D 619 CYS cc_start: 0.0969 (OUTLIER) cc_final: 0.0646 (t) REVERT: D 641 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7525 (p0) REVERT: D 650 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5934 (m-10) outliers start: 151 outliers final: 91 residues processed: 484 average time/residue: 0.3243 time to fit residues: 246.4367 Evaluate side-chains 415 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 306 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 336 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 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 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 131 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 255 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 417 HIS 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22840 Z= 0.254 Angle : 0.719 7.501 30712 Z= 0.356 Chirality : 0.041 0.169 3372 Planarity : 0.005 0.075 3736 Dihedral : 18.369 176.459 3916 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.83 % Favored : 88.02 % Rotamer: Outliers : 7.66 % Allowed : 17.64 % Favored : 74.70 % 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: -1.07 (0.17), residues: 2596 helix: 0.85 (0.13), residues: 1556 sheet: -1.78 (0.68), residues: 40 loop : -3.37 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 521 HIS 0.004 0.001 HIS A 256 PHE 0.015 0.001 PHE D 316 TYR 0.013 0.001 TYR D 451 ARG 0.006 0.001 ARG C 122 *********************** 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 527 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 349 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8241 (mtpt) REVERT: A 166 ASP cc_start: 0.7951 (t70) cc_final: 0.7568 (t0) REVERT: A 268 LEU cc_start: 0.9332 (tm) cc_final: 0.9117 (tt) REVERT: A 336 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8715 (p) REVERT: A 429 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 483 GLN cc_start: 0.7276 (tp40) cc_final: 0.6023 (tm-30) REVERT: A 541 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7740 (tp) REVERT: A 637 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5761 (pt) REVERT: A 650 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5587 (m-10) REVERT: B 121 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8177 (mtpt) REVERT: B 166 ASP cc_start: 0.8085 (t70) cc_final: 0.7667 (t0) REVERT: B 358 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8801 (tttp) REVERT: B 541 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7805 (tp) REVERT: B 578 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7734 (mmp) REVERT: B 637 ILE cc_start: 0.6008 (OUTLIER) cc_final: 0.5664 (pt) REVERT: B 641 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7772 (p0) REVERT: B 650 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5751 (m-10) REVERT: B 749 LEU cc_start: 0.8217 (tp) cc_final: 0.7997 (tt) REVERT: C 166 ASP cc_start: 0.8101 (t70) cc_final: 0.7684 (t0) REVERT: C 336 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8697 (p) REVERT: C 358 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (tttp) REVERT: C 541 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7913 (tp) REVERT: C 578 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7877 (mmp) REVERT: C 637 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5669 (pt) REVERT: C 641 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7714 (p0) REVERT: C 650 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.5663 (m-10) REVERT: D 336 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (p) REVERT: D 358 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8619 (tptt) REVERT: D 429 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7678 (mp) REVERT: D 541 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7799 (tp) REVERT: D 578 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7838 (mmp) REVERT: D 637 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5697 (pt) REVERT: D 641 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7743 (p0) REVERT: D 650 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5704 (m-10) REVERT: D 725 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7131 (pm20) outliers start: 178 outliers final: 94 residues processed: 485 average time/residue: 0.3397 time to fit residues: 263.1325 Evaluate side-chains 428 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 307 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 336 THR 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 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 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 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 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 720 LEU Chi-restraints excluded: chain B residue 723 VAL 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 336 THR 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 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 336 THR 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 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 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 233 optimal weight: 30.0000 chunk 177 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 160 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22840 Z= 0.256 Angle : 0.717 7.994 30712 Z= 0.352 Chirality : 0.041 0.164 3372 Planarity : 0.004 0.073 3736 Dihedral : 17.863 179.989 3916 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.44 % Favored : 87.40 % Rotamer: Outliers : 7.62 % Allowed : 18.46 % Favored : 73.92 % 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: 0.99 (0.13), residues: 1536 sheet: -1.44 (0.68), residues: 40 loop : -3.36 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 493 HIS 0.006 0.001 HIS B 471 PHE 0.015 0.001 PHE B 316 TYR 0.015 0.002 TYR C 540 ARG 0.007 0.001 ARG D 122 *********************** 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 506 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 329 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8267 (mtpt) REVERT: A 166 ASP cc_start: 0.7938 (t70) cc_final: 0.7598 (t0) REVERT: A 268 LEU cc_start: 0.9279 (tm) cc_final: 0.9050 (tt) REVERT: A 429 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7752 (mp) REVERT: A 541 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7753 (tp) REVERT: A 637 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5718 (pt) REVERT: A 641 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7811 (p0) REVERT: A 650 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5598 (m-10) REVERT: B 121 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8161 (mtpt) REVERT: B 166 ASP cc_start: 0.8074 (t70) cc_final: 0.7663 (t0) REVERT: B 336 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8689 (p) REVERT: B 358 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8791 (tttp) REVERT: B 541 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7818 (tp) REVERT: B 637 ILE cc_start: 0.6034 (OUTLIER) cc_final: 0.5687 (pt) REVERT: B 650 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5744 (m-10) REVERT: B 749 LEU cc_start: 0.8183 (tp) cc_final: 0.7946 (tt) REVERT: C 166 ASP cc_start: 0.8090 (t70) cc_final: 0.7676 (t0) REVERT: C 336 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8697 (p) REVERT: C 358 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8803 (tttp) REVERT: C 541 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 578 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (mmp) REVERT: C 637 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5711 (pt) REVERT: C 641 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7742 (p0) REVERT: C 650 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5720 (m-10) REVERT: D 336 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8697 (p) REVERT: D 358 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8810 (tttp) REVERT: D 429 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7643 (mp) REVERT: D 462 ARG cc_start: 0.7224 (mmt180) cc_final: 0.6303 (mmp80) REVERT: D 541 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7820 (tp) REVERT: D 578 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7819 (mmp) REVERT: D 637 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5772 (pt) REVERT: D 641 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7779 (p0) REVERT: D 650 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.5764 (m-10) REVERT: D 725 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7135 (pm20) outliers start: 177 outliers final: 109 residues processed: 476 average time/residue: 0.3130 time to fit residues: 240.1775 Evaluate side-chains 439 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 304 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 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 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 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 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 336 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 618 ASP Chi-restraints excluded: chain B residue 637 ILE 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 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 336 THR 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 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 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 336 THR 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 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 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 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 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 242 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22840 Z= 0.349 Angle : 0.753 10.579 30712 Z= 0.372 Chirality : 0.043 0.175 3372 Planarity : 0.004 0.072 3736 Dihedral : 17.285 171.524 3916 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.67 % Favored : 87.17 % Rotamer: Outliers : 7.66 % Allowed : 20.01 % Favored : 72.33 % 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: -1.06 (0.17), residues: 2596 helix: 0.94 (0.14), residues: 1536 sheet: -1.58 (0.69), residues: 40 loop : -3.43 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 493 HIS 0.005 0.001 HIS C 256 PHE 0.022 0.002 PHE B 316 TYR 0.014 0.002 TYR C 451 ARG 0.006 0.001 ARG C 122 *********************** 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 497 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 319 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8273 (mtpt) REVERT: A 166 ASP cc_start: 0.7967 (t70) cc_final: 0.7638 (t0) REVERT: A 268 LEU cc_start: 0.9312 (tm) cc_final: 0.9077 (tt) REVERT: A 429 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 541 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 637 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5848 (pt) REVERT: A 641 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7871 (p0) REVERT: A 650 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5681 (m-10) REVERT: B 121 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8122 (mtmt) REVERT: B 166 ASP cc_start: 0.8071 (t70) cc_final: 0.7683 (t0) REVERT: B 358 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8764 (tttp) REVERT: B 541 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 637 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5848 (pt) REVERT: B 641 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7861 (p0) REVERT: B 650 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5828 (m-10) REVERT: B 749 LEU cc_start: 0.8203 (tp) cc_final: 0.7952 (tt) REVERT: C 166 ASP cc_start: 0.8083 (t70) cc_final: 0.7704 (t0) REVERT: C 358 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8592 (tptt) REVERT: C 541 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7831 (tp) REVERT: C 637 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5847 (pt) REVERT: C 641 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7761 (p0) REVERT: C 650 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5715 (m-10) REVERT: D 121 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8126 (mtpt) REVERT: D 358 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8776 (tttp) REVERT: D 429 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7710 (mp) REVERT: D 541 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7809 (tp) REVERT: D 637 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5903 (pt) REVERT: D 641 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7788 (p0) REVERT: D 650 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5815 (m-10) REVERT: D 725 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7199 (pm20) outliers start: 178 outliers final: 125 residues processed: 467 average time/residue: 0.3095 time to fit residues: 230.2444 Evaluate side-chains 446 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 299 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 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 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 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 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 402 SER 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 497 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 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 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 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 488 MET 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 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 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 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 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET 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 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 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 71 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22840 Z= 0.242 Angle : 0.708 9.942 30712 Z= 0.350 Chirality : 0.042 0.155 3372 Planarity : 0.004 0.072 3736 Dihedral : 16.836 163.254 3916 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.67 % Favored : 88.17 % Rotamer: Outliers : 6.80 % Allowed : 21.77 % Favored : 71.43 % 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: -0.99 (0.17), residues: 2596 helix: 0.99 (0.14), residues: 1536 sheet: -1.52 (0.73), residues: 40 loop : -3.40 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 493 HIS 0.005 0.001 HIS A 256 PHE 0.018 0.001 PHE B 316 TYR 0.016 0.001 TYR C 540 ARG 0.005 0.000 ARG A 122 *********************** 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 475 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 317 time to evaluate : 2.437 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 121 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8244 (mtpt) REVERT: A 166 ASP cc_start: 0.7951 (t70) cc_final: 0.7619 (t0) REVERT: A 268 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9036 (tt) REVERT: A 429 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 541 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7675 (tp) REVERT: A 637 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5692 (pt) REVERT: A 646 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6308 (mt0) REVERT: A 650 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5562 (m-10) REVERT: B 121 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8100 (mtpt) REVERT: B 166 ASP cc_start: 0.8060 (t70) cc_final: 0.7677 (t0) REVERT: B 358 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8611 (tptt) REVERT: B 541 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7761 (tp) REVERT: B 618 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5196 (m-30) REVERT: B 637 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5701 (pt) REVERT: B 641 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7117 (p0) REVERT: B 650 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5638 (m-10) REVERT: B 749 LEU cc_start: 0.8182 (tp) cc_final: 0.7935 (tt) REVERT: C 121 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8132 (mtmt) REVERT: C 166 ASP cc_start: 0.8082 (t70) cc_final: 0.7700 (t0) REVERT: C 358 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8609 (tptt) REVERT: C 483 GLN cc_start: 0.7293 (tp40) cc_final: 0.5838 (tm-30) REVERT: C 541 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7792 (tp) REVERT: C 618 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.4826 (m-30) REVERT: C 637 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5723 (pt) REVERT: C 650 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5699 (m-10) REVERT: D 121 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8082 (mtpt) REVERT: D 358 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8596 (tptt) REVERT: D 429 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7663 (mp) REVERT: D 541 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7773 (tp) REVERT: D 618 ASP cc_start: 0.5980 (OUTLIER) cc_final: 0.4601 (m-30) REVERT: D 637 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5807 (pt) REVERT: D 650 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5603 (m-10) REVERT: D 725 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7910 (pm20) outliers start: 158 outliers final: 111 residues processed: 439 average time/residue: 0.3387 time to fit residues: 237.8349 Evaluate side-chains 429 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 294 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 268 LEU 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 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 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 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 646 GLN Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 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 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 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 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 488 MET 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 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 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 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 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET 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 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 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 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 211 optimal weight: 0.2980 chunk 140 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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** B 410 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22840 Z= 0.227 Angle : 0.698 9.322 30712 Z= 0.346 Chirality : 0.041 0.170 3372 Planarity : 0.004 0.071 3736 Dihedral : 16.378 162.456 3916 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 6.54 % Allowed : 22.46 % Favored : 71.00 % 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: -0.94 (0.17), residues: 2596 helix: 1.03 (0.14), residues: 1536 sheet: -1.39 (0.77), residues: 40 loop : -3.37 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 493 HIS 0.004 0.001 HIS C 256 PHE 0.020 0.001 PHE B 316 TYR 0.010 0.001 TYR B 451 ARG 0.003 0.000 ARG D 464 *********************** 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 467 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 315 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8172 (mtpt) REVERT: A 166 ASP cc_start: 0.7950 (t70) cc_final: 0.7609 (t0) REVERT: A 268 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9008 (tt) REVERT: A 429 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 618 ASP cc_start: 0.5773 (OUTLIER) cc_final: 0.4014 (m-30) REVERT: A 637 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5590 (pt) REVERT: A 650 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5559 (m-10) REVERT: B 121 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8081 (mtpt) REVERT: B 166 ASP cc_start: 0.8056 (t70) cc_final: 0.7705 (t0) REVERT: B 358 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8614 (tptt) REVERT: B 637 ILE cc_start: 0.6002 (OUTLIER) cc_final: 0.5664 (pt) REVERT: B 641 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7107 (p0) REVERT: B 650 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5587 (m-10) REVERT: B 749 LEU cc_start: 0.8196 (tp) cc_final: 0.7937 (tt) REVERT: C 121 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8102 (mtmt) REVERT: C 166 ASP cc_start: 0.8076 (t70) cc_final: 0.7672 (t0) REVERT: C 358 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8614 (tptt) REVERT: C 637 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.5645 (pt) REVERT: C 650 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5702 (m-10) REVERT: D 121 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8081 (mtmt) REVERT: D 358 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8602 (tptt) REVERT: D 429 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7701 (mp) REVERT: D 637 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5731 (pt) REVERT: D 641 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7086 (p0) REVERT: D 650 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5564 (m-10) REVERT: D 725 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7924 (pm20) outliers start: 152 outliers final: 115 residues processed: 434 average time/residue: 0.2993 time to fit residues: 208.3116 Evaluate side-chains 432 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 299 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 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 497 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU 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 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 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 497 ILE 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 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 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 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 488 MET 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 578 MET 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 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 497 ILE 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 578 MET 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 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 585 HIS ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 646 GLN C 745 HIS ** D 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS ** D 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22840 Z= 0.196 Angle : 0.698 15.783 30712 Z= 0.343 Chirality : 0.041 0.185 3372 Planarity : 0.004 0.071 3736 Dihedral : 15.977 162.332 3912 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 5.59 % Allowed : 23.62 % Favored : 70.78 % 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: -0.90 (0.17), residues: 2596 helix: 1.06 (0.14), residues: 1544 sheet: -1.40 (0.78), residues: 40 loop : -3.40 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 493 HIS 0.010 0.001 HIS C 585 PHE 0.017 0.001 PHE C 316 TYR 0.019 0.001 TYR B 540 ARG 0.008 0.000 ARG D 690 *********************** 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 457 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 327 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8185 (mtpt) REVERT: A 166 ASP cc_start: 0.7921 (t70) cc_final: 0.7574 (t0) REVERT: A 207 GLU cc_start: 0.7958 (pm20) cc_final: 0.7685 (mm-30) REVERT: A 268 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8992 (tt) REVERT: A 429 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 637 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5427 (pt) REVERT: A 650 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5443 (m-10) REVERT: A 661 TYR cc_start: 0.8667 (t80) cc_final: 0.8193 (t80) REVERT: B 121 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8015 (mtpt) REVERT: B 166 ASP cc_start: 0.8035 (t70) cc_final: 0.7698 (t0) REVERT: B 207 GLU cc_start: 0.8134 (pm20) cc_final: 0.7871 (mm-30) REVERT: B 358 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8630 (tptt) REVERT: B 431 MET cc_start: 0.7200 (mmt) cc_final: 0.6960 (mmm) REVERT: B 637 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5447 (pt) REVERT: B 650 TYR cc_start: 0.6126 (OUTLIER) cc_final: 0.5560 (m-10) REVERT: B 661 TYR cc_start: 0.8673 (t80) cc_final: 0.8194 (t80) REVERT: B 690 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7336 (mtt180) REVERT: B 749 LEU cc_start: 0.8183 (tp) cc_final: 0.7930 (tt) REVERT: C 358 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8595 (tptt) REVERT: C 637 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5435 (pt) REVERT: C 650 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5501 (m-10) REVERT: C 661 TYR cc_start: 0.8677 (t80) cc_final: 0.8198 (t80) REVERT: D 121 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8054 (mtmt) REVERT: D 207 GLU cc_start: 0.8125 (pm20) cc_final: 0.7835 (mm-30) REVERT: D 358 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8596 (tptt) REVERT: D 429 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7665 (mp) REVERT: D 637 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5542 (pt) REVERT: D 650 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5533 (m-10) REVERT: D 661 TYR cc_start: 0.8689 (t80) cc_final: 0.8214 (t80) REVERT: D 690 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7289 (mtt180) outliers start: 130 outliers final: 105 residues processed: 434 average time/residue: 0.2958 time to fit residues: 208.3370 Evaluate side-chains 416 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 297 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 THR 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 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 497 ILE 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 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE 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 290 THR 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 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 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 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 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 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 578 MET 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 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 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 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 578 MET 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 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 227 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 233 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 410 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22840 Z= 0.312 Angle : 0.757 16.827 30712 Z= 0.371 Chirality : 0.043 0.177 3372 Planarity : 0.004 0.069 3736 Dihedral : 15.861 158.438 3906 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.21 % Favored : 86.79 % Rotamer: Outliers : 6.07 % Allowed : 24.14 % Favored : 69.79 % 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: -1.06 (0.17), residues: 2596 helix: 0.95 (0.14), residues: 1544 sheet: -1.67 (0.75), residues: 40 loop : -3.48 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 493 HIS 0.005 0.001 HIS A 256 PHE 0.023 0.001 PHE B 316 TYR 0.013 0.002 TYR B 451 ARG 0.008 0.001 ARG A 690 *********************** 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 427 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 286 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8159 (mtpt) REVERT: A 429 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 637 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5814 (pt) REVERT: A 650 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5559 (m-10) REVERT: A 690 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7323 (mtt180) REVERT: B 121 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8039 (mtpt) REVERT: B 166 ASP cc_start: 0.8073 (t70) cc_final: 0.7719 (t0) REVERT: B 358 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8620 (tptt) REVERT: B 618 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.4674 (m-30) REVERT: B 637 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5955 (pt) REVERT: B 650 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5632 (m-10) REVERT: B 690 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7378 (mtt-85) REVERT: B 749 LEU cc_start: 0.8262 (tp) cc_final: 0.7977 (tt) REVERT: C 358 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8580 (tptt) REVERT: C 637 ILE cc_start: 0.6282 (OUTLIER) cc_final: 0.5923 (pt) REVERT: C 650 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: D 358 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8618 (tptt) REVERT: D 429 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7724 (mp) REVERT: D 637 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.6036 (pt) REVERT: D 650 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5560 (m-10) REVERT: D 690 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7383 (mtt180) outliers start: 141 outliers final: 109 residues processed: 407 average time/residue: 0.3024 time to fit residues: 196.5371 Evaluate side-chains 400 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 277 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 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 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 497 ILE 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 591 LEU Chi-restraints excluded: chain A residue 609 ILE 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 290 THR 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 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 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 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 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 488 MET 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 534 ILE 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 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 653 LEU 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 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 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 485 LEU Chi-restraints excluded: chain D residue 488 MET 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 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE 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 153 optimal weight: 0.9990 chunk 246 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 159 optimal weight: 0.0470 chunk 126 optimal weight: 3.9990 overall best weight: 0.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 646 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22840 Z= 0.166 Angle : 0.707 16.839 30712 Z= 0.345 Chirality : 0.040 0.193 3372 Planarity : 0.004 0.070 3736 Dihedral : 15.366 159.965 3906 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 4.78 % Allowed : 25.56 % Favored : 69.66 % 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: 1.13 (0.14), residues: 1544 sheet: -1.46 (0.78), residues: 40 loop : -3.45 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 493 HIS 0.005 0.001 HIS A 417 PHE 0.018 0.001 PHE A 316 TYR 0.009 0.001 TYR D 661 ARG 0.006 0.000 ARG A 690 ********************** 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 428 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 317 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8051 (mtpt) REVERT: A 637 ILE cc_start: 0.5492 (OUTLIER) cc_final: 0.5105 (pt) REVERT: A 650 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.5395 (m-10) REVERT: A 661 TYR cc_start: 0.8600 (t80) cc_final: 0.8157 (t80) REVERT: B 121 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8026 (mtpt) REVERT: B 166 ASP cc_start: 0.8038 (t70) cc_final: 0.7638 (t0) REVERT: B 207 GLU cc_start: 0.8113 (pm20) cc_final: 0.7911 (mm-30) REVERT: B 618 ASP cc_start: 0.5765 (OUTLIER) cc_final: 0.4552 (m-30) REVERT: B 637 ILE cc_start: 0.5571 (OUTLIER) cc_final: 0.5221 (pt) REVERT: B 650 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5491 (m-10) REVERT: B 661 TYR cc_start: 0.8622 (t80) cc_final: 0.8293 (t80) REVERT: B 690 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7362 (mtt-85) REVERT: B 749 LEU cc_start: 0.8206 (tp) cc_final: 0.7958 (tt) REVERT: C 135 LEU cc_start: 0.7732 (mm) cc_final: 0.7400 (mm) REVERT: C 207 GLU cc_start: 0.8066 (pm20) cc_final: 0.7699 (mm-30) REVERT: C 358 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8537 (tptt) REVERT: C 637 ILE cc_start: 0.5566 (OUTLIER) cc_final: 0.5221 (pt) REVERT: C 650 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5441 (m-10) REVERT: C 661 TYR cc_start: 0.8630 (t80) cc_final: 0.8298 (t80) REVERT: D 135 LEU cc_start: 0.7685 (mm) cc_final: 0.7352 (mm) REVERT: D 207 GLU cc_start: 0.8091 (pm20) cc_final: 0.7846 (mm-30) REVERT: D 429 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7631 (mp) REVERT: D 637 ILE cc_start: 0.5671 (OUTLIER) cc_final: 0.5268 (pt) REVERT: D 650 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5403 (m-10) REVERT: D 661 TYR cc_start: 0.8640 (t80) cc_final: 0.8310 (t80) REVERT: D 690 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7399 (mtt180) outliers start: 111 outliers final: 87 residues processed: 410 average time/residue: 0.2968 time to fit residues: 195.0100 Evaluate side-chains 389 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 291 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE 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 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 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 290 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU 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 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 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 154 VAL 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 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 507 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 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 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 THR 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 485 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 578 MET 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 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 163 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 212 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.0040 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN B 646 GLN C 227 GLN C 646 GLN D 646 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130529 restraints weight = 30106.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134764 restraints weight = 21567.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136523 restraints weight = 17029.280| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22840 Z= 0.167 Angle : 0.717 17.104 30712 Z= 0.348 Chirality : 0.040 0.186 3372 Planarity : 0.004 0.070 3736 Dihedral : 14.749 159.338 3892 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.33 % Favored : 88.64 % Rotamer: Outliers : 4.78 % Allowed : 25.30 % Favored : 69.92 % 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: -0.84 (0.17), residues: 2596 helix: 1.12 (0.14), residues: 1568 sheet: -3.26 (0.52), residues: 96 loop : -3.37 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 493 HIS 0.007 0.001 HIS C 471 PHE 0.018 0.001 PHE B 316 TYR 0.034 0.001 TYR C 540 ARG 0.011 0.000 ARG A 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.82 seconds wall clock time: 83 minutes 26.98 seconds (5006.98 seconds total)