Starting phenix.real_space_refine on Mon Mar 11 15:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/03_2024/7fdv_31547_neut_updated.pdb" } resolution = 3.26 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= 0.058 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 5556 2.51 5 N 1370 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 663": "NH1" <-> "NH2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8508 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4147 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 19, 'TRANS': 509} Chain breaks: 2 Chain: "D" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4147 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 19, 'TRANS': 509} Chain breaks: 2 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ATP': 1, 'CLR': 1, 'HWP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ATP': 1, 'CLR': 1, 'HWP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.93, per 1000 atoms: 0.58 Number of scatterers: 8508 At special positions: 0 Unit cell: (71.71, 99.99, 122.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 1506 8.00 N 1370 7.00 C 5556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 6 sheets defined 42.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 124 through 132 removed outlier: 4.057A pdb=" N MET A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.991A pdb=" N SER A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.582A pdb=" N MET A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.558A pdb=" N GLU A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 4.176A pdb=" N LYS A 410 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 413 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 414 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 416 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 434 through 440 removed outlier: 4.288A pdb=" N LEU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.918A pdb=" N PHE A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 478 through 487 removed outlier: 4.169A pdb=" N VAL A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 531 through 554 removed outlier: 3.637A pdb=" N LEU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 577 removed outlier: 4.062A pdb=" N PHE A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Proline residue: A 570 - end of helix removed outlier: 4.294A pdb=" N ALA A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 574 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Proline residue: A 575 - end of helix Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.823A pdb=" N ILE A 599 " --> pdb=" O MET A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.531A pdb=" N TYR A 604 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 606 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A 607 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 613 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.703A pdb=" N ILE A 653 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 654 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 655 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 657 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 658 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 661 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'D' and resid 124 through 132 removed outlier: 4.057A pdb=" N MET D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 156 No H-bonds generated for 'chain 'D' and resid 153 through 156' Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.991A pdb=" N SER D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.582A pdb=" N MET D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 264 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 281 No H-bonds generated for 'chain 'D' and resid 278 through 281' Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 321 through 330 removed outlier: 3.558A pdb=" N GLU D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 416 removed outlier: 4.176A pdb=" N LYS D 410 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE D 413 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 414 " --> pdb=" O ARG D 411 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 416 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 434 through 440 removed outlier: 4.288A pdb=" N LEU D 439 " --> pdb=" O LEU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 464 removed outlier: 3.918A pdb=" N PHE D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 474 No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 478 through 487 removed outlier: 4.169A pdb=" N VAL D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 486 " --> pdb=" O GLY D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 521 through 524 No H-bonds generated for 'chain 'D' and resid 521 through 524' Processing helix chain 'D' and resid 531 through 554 removed outlier: 3.637A pdb=" N LEU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 545 " --> pdb=" O GLY D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 577 removed outlier: 4.062A pdb=" N PHE D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Proline residue: D 570 - end of helix removed outlier: 4.294A pdb=" N ALA D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE D 574 " --> pdb=" O PRO D 570 " (cutoff:3.500A) Proline residue: D 575 - end of helix Processing helix chain 'D' and resid 591 through 593 No H-bonds generated for 'chain 'D' and resid 591 through 593' Processing helix chain 'D' and resid 595 through 599 removed outlier: 3.823A pdb=" N ILE D 599 " --> pdb=" O MET D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 removed outlier: 3.531A pdb=" N TYR D 604 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE D 606 " --> pdb=" O ARG D 603 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU D 607 " --> pdb=" O TYR D 604 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE D 613 " --> pdb=" O ILE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 663 removed outlier: 3.703A pdb=" N ILE D 653 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 655 " --> pdb=" O PHE D 652 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 657 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE D 658 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 661 " --> pdb=" O PHE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= B, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.556A pdb=" N TYR A 84 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 101 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 86 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR A 99 " --> pdb=" O VAL A 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 286 through 290 removed outlier: 3.582A pdb=" N VAL A 289 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 77 through 80 Processing sheet with id= E, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.556A pdb=" N TYR D 84 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 101 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 86 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR D 99 " --> pdb=" O VAL D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 286 through 290 removed outlier: 3.582A pdb=" N VAL D 289 " --> pdb=" O TYR D 297 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 297 " --> pdb=" O VAL D 289 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 444 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: 2.06 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1288 1.30 - 1.43: 2268 1.43 - 1.55: 5004 1.55 - 1.68: 24 1.68 - 1.81: 110 Bond restraints: 8694 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 ATP D 702 " pdb=" C5 ATP D 702 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C5 ATP D 702 " pdb=" C6 ATP D 702 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.35e+01 ... (remaining 8689 not shown) Histogram of bond angle deviations from ideal: 93.03 - 101.63: 44 101.63 - 110.23: 1910 110.23 - 118.83: 5110 118.83 - 127.44: 4640 127.44 - 136.04: 64 Bond angle restraints: 11768 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP D 702 " pdb=" O3B ATP D 702 " pdb=" PG ATP D 702 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP D 702 " pdb=" O3A ATP D 702 " pdb=" PB ATP D 702 " ideal model delta sigma weight residual 136.83 120.62 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.62 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C GLU D 635 " pdb=" CA GLU D 635 " pdb=" CB GLU D 635 " ideal model delta sigma weight residual 110.04 93.03 17.01 1.51e+00 4.39e-01 1.27e+02 ... (remaining 11763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.91: 4801 20.91 - 41.82: 419 41.82 - 62.73: 70 62.73 - 83.64: 6 83.64 - 104.55: 2 Dihedral angle restraints: 5298 sinusoidal: 2242 harmonic: 3056 Sorted by residual: dihedral pdb=" C GLU D 635 " pdb=" N GLU D 635 " pdb=" CA GLU D 635 " pdb=" CB GLU D 635 " ideal model delta harmonic sigma weight residual -122.60 -101.12 -21.48 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" C GLU A 635 " pdb=" N GLU A 635 " pdb=" CA GLU A 635 " pdb=" CB GLU A 635 " ideal model delta harmonic sigma weight residual -122.60 -102.25 -20.35 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" CA GLY A 615 " pdb=" C GLY A 615 " pdb=" N LEU A 616 " pdb=" CA LEU A 616 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1286 0.100 - 0.199: 52 0.199 - 0.298: 6 0.298 - 0.398: 4 0.398 - 0.497: 2 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C13 CLR A 703 " pdb=" C12 CLR A 703 " pdb=" C14 CLR A 703 " pdb=" C17 CLR A 703 " both_signs ideal model delta sigma weight residual False -2.93 -2.43 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C13 CLR D 701 " pdb=" C12 CLR D 701 " pdb=" C14 CLR D 701 " pdb=" C17 CLR D 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.43 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C10 CLR A 703 " pdb=" C1 CLR A 703 " pdb=" C5 CLR A 703 " pdb=" C9 CLR A 703 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1347 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 634 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C SER D 634 " -0.052 2.00e-02 2.50e+03 pdb=" O SER D 634 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU D 635 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 634 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C SER A 634 " 0.052 2.00e-02 2.50e+03 pdb=" O SER A 634 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 635 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 471 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO D 472 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 472 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 472 " 0.019 5.00e-02 4.00e+02 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 7071 3.16 - 3.74: 11945 3.74 - 4.32: 17583 4.32 - 4.90: 28997 Nonbonded interactions: 65681 Sorted by model distance: nonbonded pdb=" O GLU D 635 " pdb=" CG GLU D 635 " model vdw 2.001 3.440 nonbonded pdb=" O GLU A 635 " pdb=" CG GLU A 635 " model vdw 2.059 3.440 nonbonded pdb=" OG SER A 120 " pdb=" O3G ATP A 701 " model vdw 2.199 2.440 nonbonded pdb=" OG SER D 120 " pdb=" O3G ATP D 702 " model vdw 2.199 2.440 nonbonded pdb=" O SER A 634 " pdb=" CB GLU A 635 " model vdw 2.231 3.440 ... (remaining 65676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 72 through 675) selection = (chain 'D' and resid 72 through 675) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.280 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 25.660 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.007 0.083 8694 Z= 0.471 Angle : 1.120 19.395 11768 Z= 0.663 Chirality : 0.056 0.497 1350 Planarity : 0.004 0.034 1432 Dihedral : 15.437 104.548 3342 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.66 % Allowed : 9.69 % Favored : 89.65 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -6.08 (0.17), residues: 1046 helix: -3.89 (0.14), residues: 554 sheet: -4.92 (0.35), residues: 64 loop : -3.92 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 492 HIS 0.003 0.001 HIS A 622 PHE 0.013 0.001 PHE A 281 TYR 0.010 0.001 TYR A 441 ARG 0.004 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.055 Fit side-chains REVERT: A 326 MET cc_start: 0.8136 (tpp) cc_final: 0.7754 (mmm) REVERT: A 580 SER cc_start: 0.8732 (m) cc_final: 0.8415 (m) REVERT: D 326 MET cc_start: 0.8136 (tpp) cc_final: 0.7754 (mmm) REVERT: D 580 SER cc_start: 0.8731 (m) cc_final: 0.8415 (m) outliers start: 6 outliers final: 4 residues processed: 134 average time/residue: 0.2149 time to fit residues: 39.4294 Evaluate side-chains 98 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 635 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 630 HIS D 254 GLN D 630 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8694 Z= 0.169 Angle : 0.626 6.590 11768 Z= 0.302 Chirality : 0.042 0.131 1350 Planarity : 0.004 0.029 1432 Dihedral : 12.617 89.376 1428 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.76 % Allowed : 15.64 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.98 (0.20), residues: 1046 helix: -3.01 (0.18), residues: 538 sheet: -4.48 (0.38), residues: 64 loop : -3.37 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 492 HIS 0.002 0.000 HIS A 183 PHE 0.011 0.001 PHE D 405 TYR 0.009 0.001 TYR A 441 ARG 0.002 0.000 ARG A 618 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.866 Fit side-chains REVERT: A 196 MET cc_start: 0.7644 (mtt) cc_final: 0.7353 (mtt) REVERT: A 258 LEU cc_start: 0.8145 (pp) cc_final: 0.7592 (mt) REVERT: A 425 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8143 (tp) REVERT: A 580 SER cc_start: 0.8770 (m) cc_final: 0.8431 (m) REVERT: A 664 LEU cc_start: 0.8528 (tt) cc_final: 0.8297 (mt) REVERT: D 196 MET cc_start: 0.7643 (mtt) cc_final: 0.7353 (mtt) REVERT: D 258 LEU cc_start: 0.8147 (pp) cc_final: 0.7594 (mt) REVERT: D 425 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8145 (tp) REVERT: D 580 SER cc_start: 0.8768 (m) cc_final: 0.8428 (m) REVERT: D 664 LEU cc_start: 0.8528 (tt) cc_final: 0.8296 (mt) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 0.1730 time to fit residues: 31.4292 Evaluate side-chains 110 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN D 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 8694 Z= 0.545 Angle : 0.789 7.190 11768 Z= 0.383 Chirality : 0.049 0.169 1350 Planarity : 0.005 0.036 1432 Dihedral : 12.950 80.291 1428 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 3.74 % Allowed : 19.16 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.94 (0.20), residues: 1046 helix: -3.00 (0.18), residues: 556 sheet: -4.45 (0.38), residues: 64 loop : -3.30 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 523 HIS 0.003 0.001 HIS D 171 PHE 0.018 0.002 PHE A 281 TYR 0.012 0.002 TYR D 333 ARG 0.004 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.050 Fit side-chains REVERT: A 231 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8751 (tt) REVERT: A 326 MET cc_start: 0.8014 (mmm) cc_final: 0.7695 (mmm) REVERT: A 580 SER cc_start: 0.8763 (m) cc_final: 0.8485 (m) REVERT: D 231 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8752 (tt) REVERT: D 326 MET cc_start: 0.8014 (mmm) cc_final: 0.7693 (mmm) REVERT: D 580 SER cc_start: 0.8767 (m) cc_final: 0.8488 (m) outliers start: 34 outliers final: 16 residues processed: 124 average time/residue: 0.1788 time to fit residues: 32.5181 Evaluate side-chains 112 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN D 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8694 Z= 0.164 Angle : 0.602 9.583 11768 Z= 0.288 Chirality : 0.041 0.132 1350 Planarity : 0.004 0.030 1432 Dihedral : 11.847 88.823 1428 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.52 % Allowed : 20.93 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.30 (0.21), residues: 1046 helix: -2.47 (0.19), residues: 542 sheet: -3.92 (0.42), residues: 64 loop : -3.04 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 523 HIS 0.002 0.001 HIS D 183 PHE 0.012 0.001 PHE A 405 TYR 0.012 0.001 TYR A 672 ARG 0.001 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.926 Fit side-chains REVERT: A 179 MET cc_start: 0.8824 (mmm) cc_final: 0.8619 (mmm) REVERT: A 258 LEU cc_start: 0.8344 (pp) cc_final: 0.7518 (mt) REVERT: A 425 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 580 SER cc_start: 0.8801 (m) cc_final: 0.8481 (m) REVERT: D 179 MET cc_start: 0.8826 (mmm) cc_final: 0.8622 (mmm) REVERT: D 258 LEU cc_start: 0.8345 (pp) cc_final: 0.7519 (mt) REVERT: D 425 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 580 SER cc_start: 0.8803 (m) cc_final: 0.8483 (m) outliers start: 32 outliers final: 18 residues processed: 136 average time/residue: 0.1788 time to fit residues: 35.1811 Evaluate side-chains 124 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 0.0050 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8694 Z= 0.209 Angle : 0.630 9.292 11768 Z= 0.298 Chirality : 0.041 0.128 1350 Planarity : 0.004 0.029 1432 Dihedral : 11.416 85.713 1428 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.08 % Allowed : 22.25 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.00 (0.22), residues: 1046 helix: -2.23 (0.20), residues: 542 sheet: -3.63 (0.46), residues: 64 loop : -2.94 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 523 HIS 0.002 0.001 HIS D 183 PHE 0.012 0.001 PHE A 405 TYR 0.009 0.001 TYR A 672 ARG 0.001 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.873 Fit side-chains REVERT: A 425 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 580 SER cc_start: 0.8809 (m) cc_final: 0.8498 (m) REVERT: D 425 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7917 (tt) REVERT: D 580 SER cc_start: 0.8809 (m) cc_final: 0.8494 (m) outliers start: 28 outliers final: 20 residues processed: 120 average time/residue: 0.1798 time to fit residues: 31.3425 Evaluate side-chains 121 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8694 Z= 0.171 Angle : 0.605 9.237 11768 Z= 0.284 Chirality : 0.040 0.129 1350 Planarity : 0.003 0.029 1432 Dihedral : 10.811 79.567 1428 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.30 % Allowed : 22.47 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.65 (0.22), residues: 1046 helix: -1.95 (0.20), residues: 542 sheet: -3.29 (0.51), residues: 64 loop : -2.78 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 523 HIS 0.002 0.001 HIS A 183 PHE 0.011 0.001 PHE A 405 TYR 0.008 0.001 TYR D 672 ARG 0.001 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.921 Fit side-chains REVERT: A 167 MET cc_start: 0.6857 (pmm) cc_final: 0.6621 (pmm) REVERT: A 179 MET cc_start: 0.8808 (mmm) cc_final: 0.8580 (mmm) REVERT: A 258 LEU cc_start: 0.8300 (pp) cc_final: 0.7538 (mt) REVERT: A 326 MET cc_start: 0.8005 (mmm) cc_final: 0.7633 (mmm) REVERT: A 425 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 534 PHE cc_start: 0.9037 (t80) cc_final: 0.8806 (t80) REVERT: A 580 SER cc_start: 0.8793 (m) cc_final: 0.8502 (m) REVERT: D 167 MET cc_start: 0.6856 (pmm) cc_final: 0.6620 (pmm) REVERT: D 179 MET cc_start: 0.8806 (mmm) cc_final: 0.8580 (mmm) REVERT: D 258 LEU cc_start: 0.8302 (pp) cc_final: 0.7538 (mt) REVERT: D 326 MET cc_start: 0.8006 (mmm) cc_final: 0.7635 (mmm) REVERT: D 425 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8160 (tp) REVERT: D 534 PHE cc_start: 0.9036 (t80) cc_final: 0.8805 (t80) REVERT: D 580 SER cc_start: 0.8796 (m) cc_final: 0.8504 (m) outliers start: 30 outliers final: 24 residues processed: 126 average time/residue: 0.1976 time to fit residues: 35.4514 Evaluate side-chains 121 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8694 Z= 0.314 Angle : 0.676 8.738 11768 Z= 0.318 Chirality : 0.044 0.138 1350 Planarity : 0.004 0.028 1432 Dihedral : 10.950 83.639 1428 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.74 % Allowed : 23.02 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.67 (0.22), residues: 1046 helix: -1.98 (0.20), residues: 544 sheet: -3.24 (0.54), residues: 64 loop : -2.77 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 523 HIS 0.002 0.001 HIS D 183 PHE 0.014 0.001 PHE A 405 TYR 0.009 0.001 TYR D 441 ARG 0.001 0.000 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.052 Fit side-chains REVERT: A 178 MET cc_start: 0.8783 (mmm) cc_final: 0.8450 (mmm) REVERT: A 326 MET cc_start: 0.8168 (mmm) cc_final: 0.7653 (mmm) REVERT: A 425 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 534 PHE cc_start: 0.9066 (t80) cc_final: 0.8860 (t80) REVERT: A 580 SER cc_start: 0.8822 (m) cc_final: 0.8522 (m) REVERT: D 178 MET cc_start: 0.8787 (mmm) cc_final: 0.8450 (mmm) REVERT: D 326 MET cc_start: 0.8166 (mmm) cc_final: 0.7653 (mmm) REVERT: D 425 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8223 (tp) REVERT: D 534 PHE cc_start: 0.9064 (t80) cc_final: 0.8859 (t80) REVERT: D 580 SER cc_start: 0.8823 (m) cc_final: 0.8522 (m) outliers start: 34 outliers final: 26 residues processed: 120 average time/residue: 0.1747 time to fit residues: 30.1656 Evaluate side-chains 120 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8694 Z= 0.152 Angle : 0.617 9.366 11768 Z= 0.286 Chirality : 0.040 0.131 1350 Planarity : 0.003 0.028 1432 Dihedral : 10.097 77.231 1428 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.74 % Allowed : 23.35 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.31 (0.23), residues: 1046 helix: -1.68 (0.21), residues: 544 sheet: -3.01 (0.56), residues: 64 loop : -2.63 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 492 HIS 0.002 0.000 HIS D 183 PHE 0.010 0.001 PHE D 405 TYR 0.008 0.001 TYR D 134 ARG 0.001 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.032 Fit side-chains REVERT: A 179 MET cc_start: 0.8883 (mmm) cc_final: 0.8675 (mmm) REVERT: A 326 MET cc_start: 0.7977 (mmm) cc_final: 0.7582 (mmm) REVERT: A 425 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8158 (tp) REVERT: A 563 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7960 (mp10) REVERT: A 580 SER cc_start: 0.8773 (m) cc_final: 0.8495 (m) REVERT: D 179 MET cc_start: 0.8883 (mmm) cc_final: 0.8675 (mmm) REVERT: D 326 MET cc_start: 0.7977 (mmm) cc_final: 0.7582 (mmm) REVERT: D 425 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8158 (tp) REVERT: D 563 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8095 (mm-40) REVERT: D 580 SER cc_start: 0.8770 (m) cc_final: 0.8493 (m) outliers start: 34 outliers final: 22 residues processed: 122 average time/residue: 0.1846 time to fit residues: 32.4764 Evaluate side-chains 118 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.0470 chunk 88 optimal weight: 0.0040 chunk 93 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8694 Z= 0.138 Angle : 0.599 9.037 11768 Z= 0.277 Chirality : 0.039 0.127 1350 Planarity : 0.003 0.028 1432 Dihedral : 9.465 78.131 1428 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.30 % Allowed : 23.57 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.90 (0.24), residues: 1046 helix: -1.31 (0.22), residues: 540 sheet: -2.81 (0.59), residues: 68 loop : -2.47 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 523 HIS 0.002 0.000 HIS D 183 PHE 0.010 0.001 PHE A 405 TYR 0.007 0.001 TYR D 441 ARG 0.001 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.960 Fit side-chains REVERT: A 128 MET cc_start: 0.8265 (mmm) cc_final: 0.7829 (tpp) REVERT: A 176 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 178 MET cc_start: 0.8749 (mmm) cc_final: 0.8479 (mmm) REVERT: A 179 MET cc_start: 0.8808 (mmm) cc_final: 0.8536 (mmm) REVERT: A 326 MET cc_start: 0.7991 (mmm) cc_final: 0.7604 (mmm) REVERT: A 425 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 580 SER cc_start: 0.8777 (m) cc_final: 0.8502 (m) REVERT: D 128 MET cc_start: 0.8265 (mmm) cc_final: 0.7820 (tpp) REVERT: D 176 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8117 (mt-10) REVERT: D 178 MET cc_start: 0.8747 (mmm) cc_final: 0.8478 (mmm) REVERT: D 179 MET cc_start: 0.8808 (mmm) cc_final: 0.8535 (mmm) REVERT: D 326 MET cc_start: 0.7992 (mmm) cc_final: 0.7605 (mmm) REVERT: D 425 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8178 (tp) REVERT: D 580 SER cc_start: 0.8776 (m) cc_final: 0.8500 (m) outliers start: 30 outliers final: 22 residues processed: 124 average time/residue: 0.1893 time to fit residues: 33.7429 Evaluate side-chains 122 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8694 Z= 0.356 Angle : 0.707 9.178 11768 Z= 0.330 Chirality : 0.045 0.140 1350 Planarity : 0.004 0.029 1432 Dihedral : 10.260 81.239 1428 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.96 % Allowed : 23.79 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.18 (0.23), residues: 1046 helix: -1.64 (0.21), residues: 544 sheet: -2.65 (0.62), residues: 64 loop : -2.53 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 523 HIS 0.002 0.001 HIS A 171 PHE 0.018 0.002 PHE A 534 TYR 0.015 0.001 TYR D 672 ARG 0.002 0.000 ARG A 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 1.048 Fit side-chains REVERT: A 425 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8217 (tp) REVERT: A 580 SER cc_start: 0.8814 (m) cc_final: 0.8520 (m) REVERT: D 425 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8216 (tp) REVERT: D 580 SER cc_start: 0.8814 (m) cc_final: 0.8520 (m) outliers start: 36 outliers final: 24 residues processed: 124 average time/residue: 0.1811 time to fit residues: 32.3696 Evaluate side-chains 120 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099848 restraints weight = 12732.691| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.72 r_work: 0.3094 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8694 Z= 0.224 Angle : 0.657 10.068 11768 Z= 0.302 Chirality : 0.042 0.131 1350 Planarity : 0.003 0.028 1432 Dihedral : 9.797 79.136 1428 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.86 % Allowed : 25.11 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.05 (0.23), residues: 1046 helix: -1.52 (0.21), residues: 546 sheet: -2.78 (0.60), residues: 68 loop : -2.45 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 523 HIS 0.002 0.001 HIS D 183 PHE 0.012 0.001 PHE D 405 TYR 0.008 0.001 TYR A 134 ARG 0.001 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.49 seconds wall clock time: 32 minutes 10.83 seconds (1930.83 seconds total)