Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 18:22:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_31547_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_31547.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_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_31547/08_2023/7fdv_31547_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_31547_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_31547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_31547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_31547_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdv_31547/08_2023/7fdv_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-1.21rc1-5044/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: 4.82, per 1000 atoms: 0.57 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: 3.28 Conformation dependent library (CDL) restraints added in 1.3 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: 1.55 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: 2.05 Time building geometry restraints manager: 3.55 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: 4697 20.91 - 41.82: 367 41.82 - 62.73: 44 62.73 - 83.64: 6 83.64 - 104.55: 2 Dihedral angle restraints: 5116 sinusoidal: 2060 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 5113 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: 0.780 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: 0.000 Extract box with map and model: 3.660 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.320 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- 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 : 14.657 104.548 3160 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 % 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 *********************** 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 : 1.011 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 134 average time/residue: 0.2169 time to fit residues: 39.7170 Evaluate side-chains 98 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0991 time to fit residues: 1.9934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8694 Z= 0.181 Angle : 0.639 6.630 11768 Z= 0.307 Chirality : 0.041 0.133 1350 Planarity : 0.004 0.029 1432 Dihedral : 9.649 82.198 1236 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 1.32 % 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: -5.05 (0.20), residues: 1046 helix: -3.09 (0.17), residues: 538 sheet: -4.46 (0.38), residues: 64 loop : -3.38 (0.23), residues: 444 *********************** 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 122 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.994 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 120 average time/residue: 0.1874 time to fit residues: 32.3651 Evaluate side-chains 106 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0798 time to fit residues: 2.5214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 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 254 GLN A 303 ASN D 254 GLN D 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 8694 Z= 0.522 Angle : 0.784 7.389 11768 Z= 0.380 Chirality : 0.048 0.159 1350 Planarity : 0.004 0.036 1432 Dihedral : 9.932 85.354 1236 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer Outliers : 2.42 % 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: -4.95 (0.20), residues: 1046 helix: -3.03 (0.17), residues: 556 sheet: -4.40 (0.39), residues: 64 loop : -3.27 (0.24), residues: 426 *********************** 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 116 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.955 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 112 average time/residue: 0.1810 time to fit residues: 29.5489 Evaluate side-chains 100 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0801 time to fit residues: 2.4422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 94 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8694 Z= 0.140 Angle : 0.609 9.679 11768 Z= 0.286 Chirality : 0.040 0.133 1350 Planarity : 0.003 0.029 1432 Dihedral : 9.058 86.132 1236 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 1.98 % 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: -4.13 (0.22), residues: 1046 helix: -2.37 (0.20), residues: 542 sheet: -3.99 (0.42), residues: 68 loop : -2.87 (0.24), residues: 436 *********************** 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 128 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.877 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 126 average time/residue: 0.1877 time to fit residues: 34.0574 Evaluate side-chains 102 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0808 time to fit residues: 1.9104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 8694 Z= 0.360 Angle : 0.700 8.436 11768 Z= 0.332 Chirality : 0.044 0.137 1350 Planarity : 0.004 0.030 1432 Dihedral : 9.337 88.975 1236 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 2.86 % 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: -4.16 (0.22), residues: 1046 helix: -2.40 (0.19), residues: 554 sheet: -3.78 (0.43), residues: 64 loop : -2.93 (0.25), residues: 428 *********************** 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 124 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.995 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 118 average time/residue: 0.1742 time to fit residues: 30.0761 Evaluate side-chains 112 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0862 time to fit residues: 3.5909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.2172 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= 0.173 Angle : 0.624 9.408 11768 Z= 0.291 Chirality : 0.040 0.131 1350 Planarity : 0.003 0.027 1432 Dihedral : 8.934 87.061 1236 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 1.32 % 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: -3.75 (0.22), residues: 1046 helix: -2.10 (0.20), residues: 556 sheet: -3.52 (0.47), residues: 64 loop : -2.69 (0.25), residues: 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 112 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.043 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 0.2115 time to fit residues: 32.9493 Evaluate side-chains 107 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0925 time to fit residues: 2.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.2296 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= 0.189 Angle : 0.650 10.267 11768 Z= 0.295 Chirality : 0.041 0.130 1350 Planarity : 0.003 0.027 1432 Dihedral : 8.848 87.085 1236 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 1.10 % 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: -3.48 (0.23), residues: 1046 helix: -1.91 (0.20), residues: 556 sheet: -3.31 (0.52), residues: 64 loop : -2.53 (0.26), residues: 426 *********************** 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 114 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.907 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 110 average time/residue: 0.2056 time to fit residues: 31.5258 Evaluate side-chains 104 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1038 time to fit residues: 1.6410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 63 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8694 Z= 0.145 Angle : 0.624 9.143 11768 Z= 0.285 Chirality : 0.040 0.130 1350 Planarity : 0.003 0.027 1432 Dihedral : 8.548 84.327 1236 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.87 % 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: -3.15 (0.23), residues: 1046 helix: -1.63 (0.21), residues: 552 sheet: -2.97 (0.56), residues: 64 loop : -2.44 (0.26), residues: 430 *********************** 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 133 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.037 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 126 average time/residue: 0.2174 time to fit residues: 39.4021 Evaluate side-chains 108 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1094 time to fit residues: 2.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.0170 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 8694 Z= 0.145 Angle : 0.636 10.989 11768 Z= 0.285 Chirality : 0.040 0.129 1350 Planarity : 0.003 0.026 1432 Dihedral : 8.247 85.299 1236 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.55 % 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: -2.74 (0.24), residues: 1046 helix: -1.28 (0.22), residues: 540 sheet: -2.79 (0.58), residues: 68 loop : -2.24 (0.26), residues: 438 *********************** 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 113 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.983 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 113 average time/residue: 0.1999 time to fit residues: 32.2961 Evaluate side-chains 109 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0874 time to fit residues: 1.8295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8694 Z= 0.187 Angle : 0.667 10.705 11768 Z= 0.299 Chirality : 0.041 0.128 1350 Planarity : 0.003 0.027 1432 Dihedral : 8.048 86.024 1236 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.33 % 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: -2.66 (0.24), residues: 1046 helix: -1.22 (0.22), residues: 540 sheet: -2.63 (0.60), residues: 68 loop : -2.20 (0.26), residues: 438 ********************** 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 107 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.971 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 107 average time/residue: 0.1993 time to fit residues: 30.4820 Evaluate side-chains 102 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.126140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102661 restraints weight = 12402.536| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.63 r_work: 0.3140 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8694 Z= 0.210 Angle : 0.673 10.620 11768 Z= 0.302 Chirality : 0.041 0.130 1350 Planarity : 0.003 0.026 1432 Dihedral : 8.014 87.609 1236 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.44 % 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: -2.67 (0.24), residues: 1046 helix: -1.26 (0.22), residues: 542 sheet: -2.30 (0.63), residues: 64 loop : -2.25 (0.26), residues: 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1707.54 seconds wall clock time: 31 minutes 57.81 seconds (1917.81 seconds total)