Starting phenix.real_space_refine on Fri Apr 12 03:35:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/04_2024/8sml_40590_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/04_2024/8sml_40590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/04_2024/8sml_40590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/04_2024/8sml_40590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/04_2024/8sml_40590_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sml_40590/04_2024/8sml_40590_neut.pdb" } resolution = 3.3 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= 0.007 sd= 0.441 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 78 5.16 5 C 7894 2.51 5 N 2068 2.21 5 O 2348 1.98 5 H 12234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 8910 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 39, 'TRANS': 530} Chain breaks: 10 Chain: "B" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1573 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 8910 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 39, 'TRANS': 530} Chain breaks: 10 Chain: "E" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1573 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.05, per 1000 atoms: 0.45 Number of scatterers: 24628 At special positions: 0 Unit cell: (156.145, 122.745, 68.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 78 16.00 O 2348 8.00 N 2068 7.00 C 7894 6.00 H 12234 1.00 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: 18.44 Conformation dependent library (CDL) restraints added in 2.7 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 16.7% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.757A pdb=" N ASP A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 532 through 558 removed outlier: 3.974A pdb=" N ASN A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.628A pdb=" N LYS C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.757A pdb=" N ASP D 168 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 317 through 330 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 532 through 558 removed outlier: 3.974A pdb=" N ASN D 549 " --> pdb=" O CYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 562 No H-bonds generated for 'chain 'D' and resid 560 through 562' Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 610 through 621 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'F' and resid 64 through 67 removed outlier: 3.627A pdb=" N LYS F 67 " --> pdb=" O ASP F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 64 through 67' Processing helix chain 'F' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.854A pdb=" N ILE A 7 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.983A pdb=" N VAL A 104 " --> pdb=" O TYR A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 4.805A pdb=" N ASP A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 213 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.521A pdb=" N ALA A 148 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A 283 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP A 273 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 199 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 removed outlier: 8.084A pdb=" N VAL A 392 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 367 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.385A pdb=" N GLN A 306 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 335 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 308 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG A 650 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 308 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 648 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 removed outlier: 6.325A pdb=" N ILE A 428 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU A 462 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 430 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480 removed outlier: 8.123A pdb=" N ILE A 565 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 489 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 567 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 491 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573 Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 592 Processing sheet with id=AB3, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.542A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.138A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.189A pdb=" N GLY C 13 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 36 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C 52 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.189A pdb=" N GLY C 13 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 6 through 8 removed outlier: 6.854A pdb=" N ILE D 7 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 20 removed outlier: 3.983A pdb=" N VAL D 104 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 15 through 20 removed outlier: 4.804A pdb=" N ASP D 248 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 213 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.521A pdb=" N ALA D 148 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 283 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP D 273 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 199 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.084A pdb=" N VAL D 392 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 367 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 333 through 336 removed outlier: 6.385A pdb=" N GLN D 306 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR D 335 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 308 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG D 650 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 308 " --> pdb=" O ASN D 648 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 648 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 removed outlier: 6.326A pdb=" N ILE D 428 " --> pdb=" O VAL D 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU D 462 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE D 430 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 416 through 418 Processing sheet with id=AC8, first strand: chain 'D' and resid 476 through 480 removed outlier: 8.123A pdb=" N ILE D 565 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 489 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE D 567 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 491 " --> pdb=" O ILE D 567 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 571 through 573 Processing sheet with id=AD1, first strand: chain 'D' and resid 590 through 592 Processing sheet with id=AD2, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.139A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AD6, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.188A pdb=" N GLY F 13 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE F 36 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER F 52 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP F 38 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.188A pdb=" N GLY F 13 " --> pdb=" O THR F 123 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1230 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: 10.52 Time building geometry restraints manager: 19.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 12192 1.13 - 1.30: 2073 1.30 - 1.47: 5111 1.47 - 1.65: 5416 1.65 - 1.82: 114 Bond restraints: 24906 Sorted by residual: bond pdb=" N GLU D 556 " pdb=" H GLU D 556 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NE2 HIS C 37 " pdb=" HE2 HIS C 37 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ALA C 112 " pdb=" H ALA C 112 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N ASP B 82 " pdb=" H ASP B 82 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE1 TYR C 62 " pdb=" HE1 TYR C 62 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 24901 not shown) Histogram of bond angle deviations from ideal: 96.48 - 104.16: 240 104.16 - 111.84: 28317 111.84 - 119.52: 6762 119.52 - 127.20: 9481 127.20 - 134.88: 188 Bond angle restraints: 44988 Sorted by residual: angle pdb=" CB HIS D 245 " pdb=" CG HIS D 245 " pdb=" CD2 HIS D 245 " ideal model delta sigma weight residual 131.20 125.34 5.86 1.30e+00 5.92e-01 2.03e+01 angle pdb=" CB HIS A 245 " pdb=" CG HIS A 245 " pdb=" CD2 HIS A 245 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" C ASP A 369 " pdb=" N SER A 370 " pdb=" CA SER A 370 " ideal model delta sigma weight residual 120.60 127.44 -6.84 1.53e+00 4.27e-01 2.00e+01 angle pdb=" C ASP D 369 " pdb=" N SER D 370 " pdb=" CA SER D 370 " ideal model delta sigma weight residual 120.60 127.43 -6.83 1.53e+00 4.27e-01 1.99e+01 angle pdb=" O GLU D 170 " pdb=" C GLU D 170 " pdb=" N VAL D 171 " ideal model delta sigma weight residual 123.26 118.87 4.39 1.05e+00 9.07e-01 1.75e+01 ... (remaining 44983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10804 18.00 - 36.00: 596 36.00 - 53.99: 236 53.99 - 71.99: 172 71.99 - 89.99: 36 Dihedral angle restraints: 11844 sinusoidal: 6424 harmonic: 5420 Sorted by residual: dihedral pdb=" CA LYS D 224 " pdb=" C LYS D 224 " pdb=" N CYS D 225 " pdb=" CA CYS D 225 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LYS A 224 " pdb=" C LYS A 224 " pdb=" N CYS A 225 " pdb=" CA CYS A 225 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PHE F 108 " pdb=" C PHE F 108 " pdb=" N TRP F 109 " pdb=" CA TRP F 109 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 11841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1466 0.070 - 0.139: 363 0.139 - 0.209: 91 0.209 - 0.278: 8 0.278 - 0.348: 2 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CA SER E 52 " pdb=" N SER E 52 " pdb=" C SER E 52 " pdb=" CB SER E 52 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA SER B 52 " pdb=" N SER B 52 " pdb=" C SER B 52 " pdb=" CB SER B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASP A 169 " pdb=" N ASP A 169 " pdb=" C ASP A 169 " pdb=" CB ASP A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1927 not shown) Planarity restraints: 3666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.108 2.00e-02 2.50e+03 5.69e-02 1.29e+02 pdb=" CG TRP C 111 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP C 111 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP C 111 " -0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP C 111 " -0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 111 " 0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 111 " -0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP C 111 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 111 " -0.108 2.00e-02 2.50e+03 5.68e-02 1.29e+02 pdb=" CG TRP F 111 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP F 111 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 111 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP F 111 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP F 111 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP F 111 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 111 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 111 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP F 111 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP F 111 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP F 111 " 0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP F 111 " 0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 111 " -0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 111 " 0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP F 111 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 212 " 0.062 9.50e-02 1.11e+02 7.01e-02 1.01e+02 pdb=" NE ARG D 212 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG D 212 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG D 212 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG D 212 " -0.041 2.00e-02 2.50e+03 pdb="HH11 ARG D 212 " 0.056 2.00e-02 2.50e+03 pdb="HH12 ARG D 212 " 0.059 2.00e-02 2.50e+03 pdb="HH21 ARG D 212 " 0.139 2.00e-02 2.50e+03 pdb="HH22 ARG D 212 " -0.079 2.00e-02 2.50e+03 ... (remaining 3663 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1456 2.14 - 2.75: 41601 2.75 - 3.37: 68209 3.37 - 3.98: 94788 3.98 - 4.60: 137827 Nonbonded interactions: 343881 Sorted by model distance: nonbonded pdb=" HG SER D 161 " pdb=" H ALA D 163 " model vdw 1.519 2.100 nonbonded pdb=" HG SER A 161 " pdb=" H ALA A 163 " model vdw 1.520 2.100 nonbonded pdb=" OD1 ASP A 258 " pdb=" H THR A 259 " model vdw 1.576 1.850 nonbonded pdb=" OD1 ASP D 258 " pdb=" H THR D 259 " model vdw 1.577 1.850 nonbonded pdb=" OD1 ASP C 75 " pdb=" HG SER C 77 " model vdw 1.595 1.850 ... (remaining 343876 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 7.650 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: 0.390 Extract box with map and model: 31.110 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 77.280 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.010 0.079 12672 Z= 0.635 Angle : 1.008 8.041 17196 Z= 0.650 Chirality : 0.064 0.348 1930 Planarity : 0.007 0.063 2196 Dihedral : 11.401 89.769 4608 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.08 % Favored : 97.80 % Rotamer: Outliers : 0.14 % Allowed : 1.30 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1542 helix: 0.12 (0.35), residues: 164 sheet: 0.42 (0.21), residues: 584 loop : 0.48 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.008 TRP C 111 HIS 0.009 0.001 HIS C 37 PHE 0.072 0.003 PHE E 98 TYR 0.073 0.007 TYR F 56 ARG 0.012 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7478 (mtp) cc_final: 0.7190 (mtt) REVERT: A 572 LYS cc_start: 0.7392 (pttt) cc_final: 0.7105 (pttm) REVERT: D 572 LYS cc_start: 0.7357 (pttt) cc_final: 0.7077 (pttm) outliers start: 2 outliers final: 0 residues processed: 349 average time/residue: 0.5455 time to fit residues: 273.9134 Evaluate side-chains 192 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN D 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12672 Z= 0.274 Angle : 0.623 5.448 17196 Z= 0.338 Chirality : 0.047 0.195 1930 Planarity : 0.005 0.042 2196 Dihedral : 4.694 24.804 1686 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.02 % Allowed : 5.98 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1542 helix: 0.81 (0.38), residues: 168 sheet: 0.05 (0.20), residues: 608 loop : 0.19 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 49 HIS 0.011 0.001 HIS D 471 PHE 0.015 0.002 PHE D 285 TYR 0.012 0.002 TYR B 86 ARG 0.004 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7271 (mmp) cc_final: 0.7011 (mmm) REVERT: A 572 LYS cc_start: 0.7755 (pttt) cc_final: 0.7495 (pttm) REVERT: C 21 LEU cc_start: 0.6832 (tp) cc_final: 0.6596 (tp) REVERT: D 239 MET cc_start: 0.7236 (mmp) cc_final: 0.6969 (mmm) REVERT: D 572 LYS cc_start: 0.7736 (pttt) cc_final: 0.7466 (pttm) REVERT: F 21 LEU cc_start: 0.6911 (tp) cc_final: 0.6666 (tp) outliers start: 28 outliers final: 15 residues processed: 234 average time/residue: 0.6108 time to fit residues: 209.8232 Evaluate side-chains 198 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 461 LYS Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 245 HIS A 438 ASN A 509 HIS D 245 HIS D 509 HIS ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12672 Z= 0.281 Angle : 0.602 4.682 17196 Z= 0.326 Chirality : 0.046 0.168 1930 Planarity : 0.005 0.046 2196 Dihedral : 4.578 20.958 1686 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.87 % Allowed : 8.36 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1542 helix: 1.28 (0.39), residues: 166 sheet: -0.21 (0.20), residues: 610 loop : -0.02 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 466 HIS 0.006 0.001 HIS D 471 PHE 0.015 0.002 PHE B 98 TYR 0.021 0.002 TYR E 49 ARG 0.006 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7288 (mmp) cc_final: 0.7041 (mmm) REVERT: A 572 LYS cc_start: 0.7873 (pttt) cc_final: 0.7381 (pptt) REVERT: D 239 MET cc_start: 0.7272 (mmp) cc_final: 0.7027 (mmm) REVERT: D 572 LYS cc_start: 0.7862 (pttt) cc_final: 0.7372 (pptt) outliers start: 26 outliers final: 18 residues processed: 221 average time/residue: 0.5565 time to fit residues: 176.4152 Evaluate side-chains 208 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 461 LYS Chi-restraints excluded: chain D residue 602 PHE Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12672 Z= 0.218 Angle : 0.550 4.290 17196 Z= 0.294 Chirality : 0.044 0.164 1930 Planarity : 0.005 0.044 2196 Dihedral : 4.505 24.167 1686 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.31 % Allowed : 9.73 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1542 helix: 1.63 (0.40), residues: 166 sheet: -0.15 (0.21), residues: 572 loop : -0.17 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 49 HIS 0.003 0.001 HIS A 471 PHE 0.012 0.001 PHE D 629 TYR 0.014 0.002 TYR E 55 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7277 (mmp) cc_final: 0.7035 (mmm) REVERT: A 572 LYS cc_start: 0.7874 (pttt) cc_final: 0.7379 (pptt) REVERT: A 589 MET cc_start: 0.7306 (ptt) cc_final: 0.6875 (ptt) REVERT: D 239 MET cc_start: 0.7261 (mmp) cc_final: 0.7019 (mmm) REVERT: D 572 LYS cc_start: 0.7842 (pttt) cc_final: 0.7372 (pptt) outliers start: 32 outliers final: 25 residues processed: 212 average time/residue: 0.5358 time to fit residues: 165.6751 Evaluate side-chains 210 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 602 PHE Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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: 0.7110 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12672 Z= 0.193 Angle : 0.527 4.418 17196 Z= 0.280 Chirality : 0.044 0.161 1930 Planarity : 0.005 0.044 2196 Dihedral : 4.335 19.633 1686 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.23 % Allowed : 9.73 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1542 helix: 1.74 (0.40), residues: 166 sheet: -0.17 (0.21), residues: 574 loop : -0.15 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 658 HIS 0.004 0.001 HIS A 245 PHE 0.010 0.001 PHE D 629 TYR 0.014 0.002 TYR B 55 ARG 0.002 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7338 (mt0) cc_final: 0.7045 (mt0) REVERT: A 239 MET cc_start: 0.7308 (mmp) cc_final: 0.7059 (mmm) REVERT: A 572 LYS cc_start: 0.7843 (pttt) cc_final: 0.7363 (pptt) REVERT: D 178 GLN cc_start: 0.7333 (mt0) cc_final: 0.7013 (mt0) REVERT: D 239 MET cc_start: 0.7280 (mmp) cc_final: 0.7029 (mmm) REVERT: D 572 LYS cc_start: 0.7849 (pttt) cc_final: 0.7376 (pptt) REVERT: F 100 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5753 (ptp-170) outliers start: 31 outliers final: 24 residues processed: 205 average time/residue: 0.5353 time to fit residues: 162.9238 Evaluate side-chains 206 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7161 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12672 Z= 0.251 Angle : 0.558 4.471 17196 Z= 0.297 Chirality : 0.045 0.163 1930 Planarity : 0.005 0.045 2196 Dihedral : 4.490 24.075 1686 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.95 % Allowed : 9.80 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1542 helix: 1.67 (0.41), residues: 166 sheet: -0.23 (0.21), residues: 560 loop : -0.41 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 466 HIS 0.003 0.001 HIS D 595 PHE 0.013 0.002 PHE A 629 TYR 0.018 0.002 TYR E 55 ARG 0.003 0.000 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7340 (mt0) cc_final: 0.7107 (mt0) REVERT: A 239 MET cc_start: 0.7332 (mmp) cc_final: 0.7092 (mmm) REVERT: A 572 LYS cc_start: 0.7892 (pttt) cc_final: 0.7380 (pptt) REVERT: A 589 MET cc_start: 0.7314 (ptt) cc_final: 0.6951 (ptt) REVERT: C 45 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6249 (mttm) REVERT: C 100 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.4987 (ptp-170) REVERT: D 178 GLN cc_start: 0.7341 (mt0) cc_final: 0.7108 (mt0) REVERT: D 196 ASN cc_start: 0.6514 (m-40) cc_final: 0.6303 (m110) REVERT: D 239 MET cc_start: 0.7266 (mmp) cc_final: 0.7023 (mmm) REVERT: D 572 LYS cc_start: 0.7903 (pttt) cc_final: 0.7390 (pptt) REVERT: F 100 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.5006 (ptp-170) outliers start: 41 outliers final: 30 residues processed: 214 average time/residue: 0.5096 time to fit residues: 161.3003 Evaluate side-chains 210 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12672 Z= 0.271 Angle : 0.573 5.231 17196 Z= 0.306 Chirality : 0.045 0.165 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.591 20.601 1686 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.31 % Allowed : 9.87 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1542 helix: 1.15 (0.39), residues: 178 sheet: -0.22 (0.21), residues: 576 loop : -0.63 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 466 HIS 0.003 0.001 HIS D 595 PHE 0.013 0.002 PHE A 629 TYR 0.018 0.002 TYR B 86 ARG 0.003 0.001 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.7394 (mt0) cc_final: 0.7139 (mt0) REVERT: A 239 MET cc_start: 0.7328 (mmp) cc_final: 0.7088 (mmm) REVERT: A 572 LYS cc_start: 0.7890 (pttt) cc_final: 0.7378 (pptt) REVERT: A 589 MET cc_start: 0.7338 (ptt) cc_final: 0.6953 (ptt) REVERT: C 14 LEU cc_start: 0.7905 (tt) cc_final: 0.7652 (mp) REVERT: C 45 LYS cc_start: 0.7088 (mmtt) cc_final: 0.6242 (mtpp) REVERT: C 100 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.4982 (ptp-170) REVERT: D 80 MET cc_start: 0.4910 (mtp) cc_final: 0.2723 (tpt) REVERT: D 178 GLN cc_start: 0.7411 (mt0) cc_final: 0.7103 (mt0) REVERT: D 239 MET cc_start: 0.7317 (mmp) cc_final: 0.7089 (mmm) REVERT: D 572 LYS cc_start: 0.7905 (pttt) cc_final: 0.7394 (pptt) REVERT: F 14 LEU cc_start: 0.7999 (tt) cc_final: 0.7639 (mp) REVERT: F 45 LYS cc_start: 0.7085 (mmtt) cc_final: 0.6244 (mtpp) REVERT: F 100 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.4989 (ptp-170) outliers start: 46 outliers final: 36 residues processed: 209 average time/residue: 0.5099 time to fit residues: 157.5415 Evaluate side-chains 217 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 179 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12672 Z= 0.269 Angle : 0.573 4.405 17196 Z= 0.307 Chirality : 0.045 0.164 1930 Planarity : 0.005 0.048 2196 Dihedral : 4.704 25.766 1686 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.03 % Allowed : 10.45 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1542 helix: 1.09 (0.39), residues: 178 sheet: -0.24 (0.21), residues: 580 loop : -0.78 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 35 HIS 0.003 0.001 HIS D 245 PHE 0.013 0.002 PHE A 629 TYR 0.018 0.002 TYR B 86 ARG 0.004 0.001 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7319 (mmp) cc_final: 0.7098 (mmm) REVERT: A 572 LYS cc_start: 0.7875 (pttt) cc_final: 0.7365 (pptt) REVERT: C 14 LEU cc_start: 0.7891 (tt) cc_final: 0.7655 (mp) REVERT: C 45 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6279 (mtpp) REVERT: C 100 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.5000 (ptp-170) REVERT: D 178 GLN cc_start: 0.7414 (mt0) cc_final: 0.7185 (mt0) REVERT: D 239 MET cc_start: 0.7319 (mmp) cc_final: 0.7099 (mmm) REVERT: D 572 LYS cc_start: 0.7899 (pttt) cc_final: 0.7382 (pptt) REVERT: F 14 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7652 (mp) REVERT: F 45 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6277 (mtpp) REVERT: F 100 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.5015 (ptp-170) outliers start: 42 outliers final: 36 residues processed: 214 average time/residue: 0.5122 time to fit residues: 162.2991 Evaluate side-chains 219 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 150 optimal weight: 0.0010 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12672 Z= 0.265 Angle : 0.577 4.635 17196 Z= 0.309 Chirality : 0.045 0.163 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.677 19.718 1686 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.88 % Allowed : 11.24 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1542 helix: 1.13 (0.40), residues: 178 sheet: -0.25 (0.21), residues: 576 loop : -0.78 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 466 HIS 0.003 0.001 HIS D 245 PHE 0.013 0.002 PHE A 629 TYR 0.018 0.002 TYR B 86 ARG 0.003 0.001 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7329 (mmp) cc_final: 0.7116 (mmm) REVERT: A 572 LYS cc_start: 0.7884 (pttt) cc_final: 0.7353 (pptt) REVERT: C 14 LEU cc_start: 0.7932 (tt) cc_final: 0.7701 (mp) REVERT: C 45 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6308 (mtpp) REVERT: C 100 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.5018 (ptp-170) REVERT: D 178 GLN cc_start: 0.7451 (mt0) cc_final: 0.7242 (mt0) REVERT: D 239 MET cc_start: 0.7330 (mmp) cc_final: 0.7123 (mmm) REVERT: D 572 LYS cc_start: 0.7880 (pttt) cc_final: 0.7380 (pptt) REVERT: F 14 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7654 (mp) REVERT: F 45 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6347 (mtpp) REVERT: F 100 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.5023 (ptp-170) outliers start: 40 outliers final: 33 residues processed: 210 average time/residue: 0.5319 time to fit residues: 164.8268 Evaluate side-chains 212 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 157 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12672 Z= 0.275 Angle : 0.582 6.410 17196 Z= 0.311 Chirality : 0.045 0.163 1930 Planarity : 0.005 0.049 2196 Dihedral : 4.759 26.113 1686 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.74 % Allowed : 11.53 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1542 helix: 1.51 (0.40), residues: 166 sheet: -0.30 (0.21), residues: 584 loop : -0.83 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 466 HIS 0.003 0.001 HIS A 595 PHE 0.015 0.002 PHE D 629 TYR 0.016 0.002 TYR B 86 ARG 0.003 0.001 ARG A 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.5099 (mtp) cc_final: 0.4894 (mtp) REVERT: A 239 MET cc_start: 0.7336 (mmp) cc_final: 0.7129 (mmm) REVERT: A 485 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7398 (mmtm) REVERT: A 572 LYS cc_start: 0.7866 (pttt) cc_final: 0.7349 (pptt) REVERT: C 14 LEU cc_start: 0.7945 (tt) cc_final: 0.7713 (mp) REVERT: C 45 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6339 (mtpp) REVERT: C 100 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.5048 (ptp-170) REVERT: D 239 MET cc_start: 0.7330 (mmp) cc_final: 0.7122 (mmm) REVERT: D 485 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7392 (mmtm) REVERT: D 572 LYS cc_start: 0.7863 (pttt) cc_final: 0.7355 (pptt) REVERT: F 14 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7696 (mp) REVERT: F 45 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6348 (mtpp) REVERT: F 100 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.5054 (ptp-170) outliers start: 38 outliers final: 33 residues processed: 209 average time/residue: 0.5280 time to fit residues: 163.7387 Evaluate side-chains 220 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 34 TYR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 128 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 7 optimal weight: 0.0770 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN D 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.181581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139847 restraints weight = 36157.287| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.60 r_work: 0.3737 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12672 Z= 0.141 Angle : 0.519 8.681 17196 Z= 0.272 Chirality : 0.044 0.160 1930 Planarity : 0.005 0.047 2196 Dihedral : 4.331 20.170 1686 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.94 % Allowed : 13.40 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1542 helix: 2.00 (0.40), residues: 166 sheet: -0.14 (0.21), residues: 612 loop : -0.63 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 658 HIS 0.003 0.001 HIS A 444 PHE 0.008 0.001 PHE A 576 TYR 0.017 0.001 TYR E 55 ARG 0.002 0.000 ARG C 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.69 seconds wall clock time: 118 minutes 4.38 seconds (7084.38 seconds total)