Starting phenix.real_space_refine on Sun Feb 18 08:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yid_33855/02_2024/7yid_33855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yid_33855/02_2024/7yid_33855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yid_33855/02_2024/7yid_33855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yid_33855/02_2024/7yid_33855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yid_33855/02_2024/7yid_33855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yid_33855/02_2024/7yid_33855.pdb" } resolution = 3.4 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= 0.000 sd= 0.059 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 K 6 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 377": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21326 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 6} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 12.05, per 1000 atoms: 0.57 Number of scatterers: 21326 At special positions: 0 Unit cell: (157.065, 157.065, 130.746, 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) K 6 19.00 S 128 16.00 O 3852 8.00 N 3544 7.00 C 13796 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: 8.90 Conformation dependent library (CDL) restraints added in 3.8 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 54.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.317A pdb=" N ARG A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 345 through 375 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS A 619 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 620 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.318A pdb=" N ARG B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 345 through 375 Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 484 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS B 619 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 620 " --> pdb=" O PHE B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.317A pdb=" N ARG C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL C 334 " --> pdb=" O ARG C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 345 through 375 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 495 removed outlier: 3.518A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 517 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS C 619 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 620 " --> pdb=" O PHE C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 643 through 653 Processing helix chain 'C' and resid 654 through 664 Processing helix chain 'C' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 688 " --> pdb=" O LYS C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.318A pdb=" N ARG D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 375 Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS D 619 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 620 " --> pdb=" O PHE D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 620' Processing helix chain 'D' and resid 643 through 653 Processing helix chain 'D' and resid 654 through 664 Processing helix chain 'D' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 595 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 606 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL A 584 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 624 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 595 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 606 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 597 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL B 584 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B 624 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 595 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE C 606 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 597 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL C 584 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA C 624 " --> pdb=" O VAL C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.647A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 93 through 98 Processing sheet with id=AB9, first strand: chain 'D' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 595 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE D 606 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 597 " --> pdb=" O VAL D 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL D 584 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA D 624 " --> pdb=" O VAL D 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 1004 hydrogen bonds defined for protein. 2916 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: 7.51 Time building geometry restraints manager: 9.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6668 1.34 - 1.46: 3354 1.46 - 1.57: 11590 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N GLN B 567 " pdb=" CA GLN B 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN C 567 " pdb=" CA GLN C 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C MET D 474 " pdb=" O MET D 474 " ideal model delta sigma weight residual 1.236 1.250 -0.015 1.28e-02 6.10e+03 1.32e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.51: 304 105.51 - 112.62: 11664 112.62 - 119.74: 7097 119.74 - 126.85: 10231 126.85 - 133.97: 288 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ASP B 531 " pdb=" CA ASP B 531 " pdb=" C ASP B 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP D 531 " pdb=" CA ASP D 531 " pdb=" C ASP D 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP A 531 " pdb=" CA ASP A 531 " pdb=" C ASP A 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP C 531 " pdb=" CA ASP C 531 " pdb=" C ASP C 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" C PHE D 566 " pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 11596 17.67 - 35.34: 1132 35.34 - 53.01: 168 53.01 - 70.68: 24 70.68 - 88.35: 12 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO D 529 " pdb=" C PRO D 529 " pdb=" N LYS D 530 " pdb=" CA LYS D 530 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO B 529 " pdb=" C PRO B 529 " pdb=" N LYS B 530 " pdb=" CA LYS B 530 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO C 529 " pdb=" C PRO C 529 " pdb=" N LYS C 530 " pdb=" CA LYS C 530 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1962 0.030 - 0.060: 953 0.060 - 0.091: 361 0.091 - 0.121: 112 0.121 - 0.151: 16 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA MET B 286 " pdb=" N MET B 286 " pdb=" C MET B 286 " pdb=" CB MET B 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA MET A 286 " pdb=" N MET A 286 " pdb=" C MET A 286 " pdb=" CB MET A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 460 " 0.020 2.00e-02 2.50e+03 1.38e-02 3.81e+00 pdb=" CG TYR B 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 460 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 460 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 460 " 0.020 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR A 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 460 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 460 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 460 " 0.020 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR C 460 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 460 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 460 " 0.004 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 5406 2.80 - 3.39: 23084 3.39 - 3.97: 37651 3.97 - 4.56: 52724 4.56 - 5.14: 79781 Nonbonded interactions: 198646 Sorted by model distance: nonbonded pdb=" O LYS A 144 " pdb=" OG1 THR A 147 " model vdw 2.216 2.440 nonbonded pdb=" O LYS C 144 " pdb=" OG1 THR C 147 " model vdw 2.216 2.440 nonbonded pdb=" O LYS B 144 " pdb=" OG1 THR B 147 " model vdw 2.216 2.440 nonbonded pdb=" O LYS D 144 " pdb=" OG1 THR D 147 " model vdw 2.216 2.440 nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR C 195 " model vdw 2.257 2.440 ... (remaining 198641 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 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.330 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 59.150 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.120 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.003 0.037 21804 Z= 0.175 Angle : 0.558 7.324 29584 Z= 0.312 Chirality : 0.041 0.151 3404 Planarity : 0.003 0.040 3668 Dihedral : 13.957 88.352 7884 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.75 (0.17), residues: 2616 helix: 1.00 (0.15), residues: 1276 sheet: -1.61 (0.31), residues: 260 loop : -2.09 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 367 HIS 0.003 0.001 HIS B 118 PHE 0.018 0.002 PHE A 566 TYR 0.033 0.001 TYR B 460 ARG 0.003 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.494 Fit side-chains REVERT: A 601 ASP cc_start: 0.6927 (t0) cc_final: 0.6485 (t0) REVERT: B 601 ASP cc_start: 0.6939 (t0) cc_final: 0.6496 (t0) REVERT: C 601 ASP cc_start: 0.6918 (t0) cc_final: 0.6480 (t0) REVERT: D 601 ASP cc_start: 0.6925 (t0) cc_final: 0.6485 (t0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3025 time to fit residues: 116.4510 Evaluate side-chains 204 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 403 ASN B 267 HIS B 403 ASN C 267 HIS C 403 ASN D 267 HIS D 403 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21804 Z= 0.265 Angle : 0.546 8.594 29584 Z= 0.296 Chirality : 0.042 0.155 3404 Planarity : 0.003 0.039 3668 Dihedral : 4.329 24.685 2864 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.73 % Favored : 92.97 % Rotamer: Outliers : 0.34 % Allowed : 8.57 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2616 helix: 0.87 (0.15), residues: 1344 sheet: -1.76 (0.31), residues: 264 loop : -2.33 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.006 0.001 HIS D 570 PHE 0.014 0.002 PHE B 660 TYR 0.032 0.001 TYR A 460 ARG 0.002 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 2.405 Fit side-chains REVERT: A 373 TYR cc_start: 0.7857 (t80) cc_final: 0.7575 (t80) REVERT: A 601 ASP cc_start: 0.6921 (t0) cc_final: 0.6512 (t0) REVERT: B 373 TYR cc_start: 0.7836 (t80) cc_final: 0.7551 (t80) REVERT: B 601 ASP cc_start: 0.6932 (t0) cc_final: 0.6521 (t0) REVERT: C 373 TYR cc_start: 0.7807 (t80) cc_final: 0.7525 (t80) REVERT: C 601 ASP cc_start: 0.6956 (t0) cc_final: 0.6530 (t0) REVERT: D 373 TYR cc_start: 0.7806 (t80) cc_final: 0.7522 (t80) REVERT: D 601 ASP cc_start: 0.6960 (t0) cc_final: 0.6531 (t0) outliers start: 8 outliers final: 4 residues processed: 204 average time/residue: 0.3134 time to fit residues: 101.9861 Evaluate side-chains 200 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain D residue 386 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.188 Angle : 0.479 5.142 29584 Z= 0.262 Chirality : 0.040 0.140 3404 Planarity : 0.003 0.035 3668 Dihedral : 4.152 22.953 2864 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 1.18 % Allowed : 12.27 % Favored : 86.55 % 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: -0.65 (0.17), residues: 2616 helix: 1.14 (0.15), residues: 1340 sheet: -1.65 (0.32), residues: 260 loop : -2.31 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 367 HIS 0.005 0.001 HIS C 570 PHE 0.012 0.001 PHE D 471 TYR 0.023 0.001 TYR B 460 ARG 0.002 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 2.538 Fit side-chains REVERT: A 64 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8135 (m) REVERT: A 286 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6364 (pmm) REVERT: A 373 TYR cc_start: 0.7865 (t80) cc_final: 0.7591 (t80) REVERT: A 601 ASP cc_start: 0.6886 (t0) cc_final: 0.6528 (t0) REVERT: A 677 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7189 (ttp80) REVERT: B 64 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8135 (m) REVERT: B 286 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6366 (pmm) REVERT: B 373 TYR cc_start: 0.7837 (t80) cc_final: 0.7562 (t80) REVERT: B 601 ASP cc_start: 0.6894 (t0) cc_final: 0.6532 (t0) REVERT: B 677 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7183 (ttp80) REVERT: C 64 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (m) REVERT: C 286 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6363 (pmm) REVERT: C 373 TYR cc_start: 0.7813 (t80) cc_final: 0.7538 (t80) REVERT: C 601 ASP cc_start: 0.6881 (t0) cc_final: 0.6522 (t0) REVERT: C 677 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7181 (ttp80) REVERT: D 64 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8128 (m) REVERT: D 286 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6354 (pmm) REVERT: D 373 TYR cc_start: 0.7811 (t80) cc_final: 0.7534 (t80) REVERT: D 601 ASP cc_start: 0.6883 (t0) cc_final: 0.6523 (t0) REVERT: D 677 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7184 (ttp80) outliers start: 28 outliers final: 8 residues processed: 224 average time/residue: 0.3212 time to fit residues: 113.6953 Evaluate side-chains 208 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 68 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: 0.7763 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21804 Z= 0.211 Angle : 0.490 6.243 29584 Z= 0.265 Chirality : 0.040 0.138 3404 Planarity : 0.003 0.034 3668 Dihedral : 4.146 23.868 2864 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.73 % Favored : 92.97 % Rotamer: Outliers : 1.85 % Allowed : 12.77 % Favored : 85.38 % 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: -0.69 (0.17), residues: 2616 helix: 1.15 (0.15), residues: 1340 sheet: -2.07 (0.40), residues: 148 loop : -2.32 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 367 HIS 0.005 0.001 HIS B 570 PHE 0.012 0.001 PHE C 660 TYR 0.021 0.001 TYR A 460 ARG 0.001 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 2.572 Fit side-chains REVERT: A 64 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8239 (m) REVERT: A 107 PHE cc_start: 0.7826 (m-80) cc_final: 0.7615 (m-80) REVERT: A 286 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6129 (pmm) REVERT: A 373 TYR cc_start: 0.7908 (t80) cc_final: 0.7625 (t80) REVERT: A 601 ASP cc_start: 0.6935 (t0) cc_final: 0.6565 (t0) REVERT: B 64 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8239 (m) REVERT: B 107 PHE cc_start: 0.7821 (m-80) cc_final: 0.7613 (m-80) REVERT: B 286 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6127 (pmm) REVERT: B 373 TYR cc_start: 0.7879 (t80) cc_final: 0.7595 (t80) REVERT: B 601 ASP cc_start: 0.6944 (t0) cc_final: 0.6572 (t0) REVERT: C 64 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8231 (m) REVERT: C 107 PHE cc_start: 0.7823 (m-80) cc_final: 0.7608 (m-80) REVERT: C 286 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6127 (pmm) REVERT: C 373 TYR cc_start: 0.7853 (t80) cc_final: 0.7571 (t80) REVERT: C 601 ASP cc_start: 0.6926 (t0) cc_final: 0.6557 (t0) REVERT: D 64 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8231 (m) REVERT: D 107 PHE cc_start: 0.7826 (m-80) cc_final: 0.7617 (m-80) REVERT: D 286 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6122 (pmm) REVERT: D 373 TYR cc_start: 0.7851 (t80) cc_final: 0.7568 (t80) REVERT: D 601 ASP cc_start: 0.6930 (t0) cc_final: 0.6562 (t0) outliers start: 44 outliers final: 24 residues processed: 232 average time/residue: 0.3128 time to fit residues: 115.1077 Evaluate side-chains 220 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21804 Z= 0.357 Angle : 0.588 8.941 29584 Z= 0.316 Chirality : 0.044 0.153 3404 Planarity : 0.003 0.039 3668 Dihedral : 4.460 25.612 2864 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.26 % Favored : 91.44 % Rotamer: Outliers : 2.56 % Allowed : 13.07 % Favored : 84.37 % 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: -0.96 (0.17), residues: 2616 helix: 0.85 (0.15), residues: 1348 sheet: -2.30 (0.40), residues: 152 loop : -2.34 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 388 HIS 0.006 0.001 HIS B 570 PHE 0.019 0.002 PHE D 660 TYR 0.024 0.002 TYR A 460 ARG 0.002 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 180 time to evaluate : 2.689 Fit side-chains REVERT: A 107 PHE cc_start: 0.7956 (m-80) cc_final: 0.7742 (m-80) REVERT: A 286 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6369 (pmm) REVERT: A 373 TYR cc_start: 0.7881 (t80) cc_final: 0.7540 (t80) REVERT: A 377 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7363 (p0) REVERT: A 601 ASP cc_start: 0.7017 (t0) cc_final: 0.6608 (t0) REVERT: B 107 PHE cc_start: 0.7950 (m-80) cc_final: 0.7735 (m-80) REVERT: B 286 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6369 (pmm) REVERT: B 373 TYR cc_start: 0.7856 (t80) cc_final: 0.7512 (t80) REVERT: B 377 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7367 (p0) REVERT: B 601 ASP cc_start: 0.7026 (t0) cc_final: 0.6617 (t0) REVERT: C 107 PHE cc_start: 0.7951 (m-80) cc_final: 0.7733 (m-80) REVERT: C 286 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6369 (pmm) REVERT: C 373 TYR cc_start: 0.7828 (t80) cc_final: 0.7490 (t80) REVERT: C 377 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7341 (p0) REVERT: C 601 ASP cc_start: 0.7010 (t0) cc_final: 0.6602 (t0) REVERT: D 107 PHE cc_start: 0.7948 (m-80) cc_final: 0.7734 (m-80) REVERT: D 286 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6362 (pmm) REVERT: D 373 TYR cc_start: 0.7829 (t80) cc_final: 0.7487 (t80) REVERT: D 377 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7344 (p0) REVERT: D 601 ASP cc_start: 0.7013 (t0) cc_final: 0.6608 (t0) outliers start: 61 outliers final: 36 residues processed: 232 average time/residue: 0.2806 time to fit residues: 107.9542 Evaluate side-chains 216 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.0980 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.188 Angle : 0.493 7.529 29584 Z= 0.266 Chirality : 0.040 0.148 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.210 22.764 2864 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 2.52 % Allowed : 13.87 % Favored : 83.61 % 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: -0.66 (0.17), residues: 2616 helix: 1.17 (0.15), residues: 1340 sheet: -2.07 (0.41), residues: 152 loop : -2.30 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 367 HIS 0.004 0.001 HIS D 570 PHE 0.012 0.002 PHE A 93 TYR 0.015 0.001 TYR B 460 ARG 0.002 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 172 time to evaluate : 2.486 Fit side-chains REVERT: A 107 PHE cc_start: 0.7906 (m-80) cc_final: 0.7670 (m-80) REVERT: A 286 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6161 (pmm) REVERT: A 373 TYR cc_start: 0.7875 (t80) cc_final: 0.7532 (t80) REVERT: A 377 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7281 (p0) REVERT: A 601 ASP cc_start: 0.7020 (t0) cc_final: 0.6606 (t0) REVERT: B 107 PHE cc_start: 0.7901 (m-80) cc_final: 0.7664 (m-80) REVERT: B 286 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6164 (pmm) REVERT: B 373 TYR cc_start: 0.7851 (t80) cc_final: 0.7504 (t80) REVERT: B 377 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 601 ASP cc_start: 0.7024 (t0) cc_final: 0.6610 (t0) REVERT: C 107 PHE cc_start: 0.7904 (m-80) cc_final: 0.7663 (m-80) REVERT: C 286 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6162 (pmm) REVERT: C 373 TYR cc_start: 0.7823 (t80) cc_final: 0.7479 (t80) REVERT: C 377 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7263 (p0) REVERT: C 601 ASP cc_start: 0.7010 (t0) cc_final: 0.6598 (t0) REVERT: D 107 PHE cc_start: 0.7901 (m-80) cc_final: 0.7666 (m-80) REVERT: D 286 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6153 (pmm) REVERT: D 373 TYR cc_start: 0.7820 (t80) cc_final: 0.7476 (t80) REVERT: D 377 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7266 (p0) REVERT: D 601 ASP cc_start: 0.7011 (t0) cc_final: 0.6602 (t0) outliers start: 60 outliers final: 32 residues processed: 220 average time/residue: 0.3004 time to fit residues: 107.8467 Evaluate side-chains 208 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 0.0170 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 overall best weight: 0.6162 ------------------------------------------------------------------------------- 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: 0.7736 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.156 Angle : 0.487 8.956 29584 Z= 0.257 Chirality : 0.040 0.139 3404 Planarity : 0.003 0.031 3668 Dihedral : 4.039 22.715 2864 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.43 % Rotamer: Outliers : 2.35 % Allowed : 14.29 % Favored : 83.36 % 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: -0.47 (0.17), residues: 2616 helix: 1.35 (0.15), residues: 1340 sheet: -1.82 (0.42), residues: 148 loop : -2.27 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 367 HIS 0.004 0.001 HIS D 570 PHE 0.014 0.001 PHE D 93 TYR 0.013 0.001 TYR C 460 ARG 0.002 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 180 time to evaluate : 2.671 Fit side-chains REVERT: A 107 PHE cc_start: 0.7830 (m-80) cc_final: 0.7604 (m-80) REVERT: A 286 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6060 (pmm) REVERT: A 373 TYR cc_start: 0.7938 (t80) cc_final: 0.7556 (t80) REVERT: A 377 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7268 (p0) REVERT: A 601 ASP cc_start: 0.7043 (t0) cc_final: 0.6628 (t0) REVERT: B 107 PHE cc_start: 0.7824 (m-80) cc_final: 0.7600 (m-80) REVERT: B 286 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6058 (pmm) REVERT: B 373 TYR cc_start: 0.7895 (t80) cc_final: 0.7514 (t80) REVERT: B 377 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7271 (p0) REVERT: B 601 ASP cc_start: 0.7041 (t0) cc_final: 0.6630 (t0) REVERT: C 107 PHE cc_start: 0.7828 (m-80) cc_final: 0.7601 (m-80) REVERT: C 286 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6055 (pmm) REVERT: C 373 TYR cc_start: 0.7866 (t80) cc_final: 0.7488 (t80) REVERT: C 377 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7250 (p0) REVERT: C 601 ASP cc_start: 0.7030 (t0) cc_final: 0.6619 (t0) REVERT: D 107 PHE cc_start: 0.7823 (m-80) cc_final: 0.7599 (m-80) REVERT: D 286 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6049 (pmm) REVERT: D 373 TYR cc_start: 0.7881 (t80) cc_final: 0.7496 (t80) REVERT: D 377 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7252 (p0) REVERT: D 601 ASP cc_start: 0.7033 (t0) cc_final: 0.6621 (t0) outliers start: 56 outliers final: 32 residues processed: 224 average time/residue: 0.3213 time to fit residues: 114.6052 Evaluate side-chains 200 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 231 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.144 Angle : 0.482 8.591 29584 Z= 0.253 Chirality : 0.039 0.143 3404 Planarity : 0.003 0.028 3668 Dihedral : 3.961 22.367 2864 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.43 % Rotamer: Outliers : 2.18 % Allowed : 14.45 % Favored : 83.36 % 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: -0.36 (0.17), residues: 2616 helix: 1.47 (0.15), residues: 1332 sheet: -1.80 (0.42), residues: 148 loop : -2.22 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 367 HIS 0.004 0.001 HIS C 570 PHE 0.013 0.001 PHE A 93 TYR 0.012 0.001 TYR B 460 ARG 0.005 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 2.540 Fit side-chains REVERT: A 107 PHE cc_start: 0.7816 (m-80) cc_final: 0.7608 (m-80) REVERT: A 286 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6039 (pmm) REVERT: A 373 TYR cc_start: 0.7912 (t80) cc_final: 0.7500 (t80) REVERT: A 377 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7289 (p0) REVERT: A 601 ASP cc_start: 0.7058 (t0) cc_final: 0.6639 (t0) REVERT: B 107 PHE cc_start: 0.7806 (m-80) cc_final: 0.7601 (m-80) REVERT: B 286 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6040 (pmm) REVERT: B 373 TYR cc_start: 0.7881 (t80) cc_final: 0.7468 (t80) REVERT: B 377 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7292 (p0) REVERT: B 601 ASP cc_start: 0.7061 (t0) cc_final: 0.6644 (t0) REVERT: C 107 PHE cc_start: 0.7811 (m-80) cc_final: 0.7602 (m-80) REVERT: C 286 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6039 (pmm) REVERT: C 373 TYR cc_start: 0.7856 (t80) cc_final: 0.7441 (t80) REVERT: C 377 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7271 (p0) REVERT: C 601 ASP cc_start: 0.7045 (t0) cc_final: 0.6630 (t0) REVERT: D 107 PHE cc_start: 0.7809 (m-80) cc_final: 0.7604 (m-80) REVERT: D 286 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6028 (pmm) REVERT: D 373 TYR cc_start: 0.7851 (t80) cc_final: 0.7436 (t80) REVERT: D 377 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7274 (p0) REVERT: D 601 ASP cc_start: 0.7050 (t0) cc_final: 0.6635 (t0) outliers start: 52 outliers final: 36 residues processed: 217 average time/residue: 0.2987 time to fit residues: 105.8969 Evaluate side-chains 217 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 chunk 237 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 0.0980 chunk 72 optimal weight: 10.0000 chunk 214 optimal weight: 30.0000 chunk 224 optimal weight: 0.0370 chunk 236 optimal weight: 0.0870 chunk 155 optimal weight: 8.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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: 0.7670 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.116 Angle : 0.466 8.436 29584 Z= 0.243 Chirality : 0.039 0.142 3404 Planarity : 0.002 0.025 3668 Dihedral : 3.844 21.933 2864 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.38 % Favored : 93.31 % Rotamer: Outliers : 1.68 % Allowed : 14.79 % Favored : 83.53 % 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: -0.20 (0.17), residues: 2616 helix: 1.61 (0.15), residues: 1332 sheet: -1.77 (0.42), residues: 148 loop : -2.14 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 513 HIS 0.003 0.001 HIS D 570 PHE 0.014 0.001 PHE D 93 TYR 0.010 0.001 TYR C 368 ARG 0.005 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 2.321 Fit side-chains REVERT: A 107 PHE cc_start: 0.7761 (m-80) cc_final: 0.7547 (m-80) REVERT: A 286 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6006 (pmm) REVERT: A 373 TYR cc_start: 0.7922 (t80) cc_final: 0.7528 (t80) REVERT: A 377 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7262 (p0) REVERT: A 601 ASP cc_start: 0.7036 (t0) cc_final: 0.6628 (t0) REVERT: B 107 PHE cc_start: 0.7750 (m-80) cc_final: 0.7537 (m-80) REVERT: B 286 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6002 (pmm) REVERT: B 373 TYR cc_start: 0.7891 (t80) cc_final: 0.7495 (t80) REVERT: B 377 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7264 (p0) REVERT: B 601 ASP cc_start: 0.7040 (t0) cc_final: 0.6634 (t0) REVERT: C 107 PHE cc_start: 0.7756 (m-80) cc_final: 0.7539 (m-80) REVERT: C 286 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6003 (pmm) REVERT: C 373 TYR cc_start: 0.7872 (t80) cc_final: 0.7475 (t80) REVERT: C 377 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7245 (p0) REVERT: C 601 ASP cc_start: 0.7013 (t0) cc_final: 0.6616 (t0) REVERT: D 107 PHE cc_start: 0.7751 (m-80) cc_final: 0.7537 (m-80) REVERT: D 286 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.5996 (pmm) REVERT: D 373 TYR cc_start: 0.7864 (t80) cc_final: 0.7465 (t80) REVERT: D 377 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7249 (p0) REVERT: D 601 ASP cc_start: 0.7024 (t0) cc_final: 0.6623 (t0) outliers start: 40 outliers final: 28 residues processed: 209 average time/residue: 0.2925 time to fit residues: 99.6282 Evaluate side-chains 205 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0770 chunk 153 optimal weight: 0.7980 chunk 118 optimal weight: 0.0980 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21804 Z= 0.139 Angle : 0.472 8.165 29584 Z= 0.248 Chirality : 0.039 0.142 3404 Planarity : 0.002 0.027 3668 Dihedral : 3.823 22.635 2864 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.96 % Favored : 93.73 % Rotamer: Outliers : 1.60 % Allowed : 14.54 % Favored : 83.87 % 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: -0.11 (0.17), residues: 2616 helix: 1.61 (0.15), residues: 1336 sheet: -1.40 (0.34), residues: 260 loop : -2.09 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 367 HIS 0.004 0.001 HIS C 570 PHE 0.012 0.001 PHE A 93 TYR 0.011 0.001 TYR C 460 ARG 0.005 0.000 ARG D 677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 2.575 Fit side-chains REVERT: A 107 PHE cc_start: 0.7836 (m-80) cc_final: 0.7612 (m-80) REVERT: A 286 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.5981 (pmm) REVERT: A 373 TYR cc_start: 0.7954 (t80) cc_final: 0.7563 (t80) REVERT: A 377 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7274 (p0) REVERT: A 601 ASP cc_start: 0.7040 (t0) cc_final: 0.6623 (t0) REVERT: B 107 PHE cc_start: 0.7823 (m-80) cc_final: 0.7601 (m-80) REVERT: B 286 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.5979 (pmm) REVERT: B 373 TYR cc_start: 0.7925 (t80) cc_final: 0.7532 (t80) REVERT: B 377 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7276 (p0) REVERT: B 601 ASP cc_start: 0.7045 (t0) cc_final: 0.6630 (t0) REVERT: C 107 PHE cc_start: 0.7829 (m-80) cc_final: 0.7604 (m-80) REVERT: C 286 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.5977 (pmm) REVERT: C 373 TYR cc_start: 0.7904 (t80) cc_final: 0.7510 (t80) REVERT: C 377 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7256 (p0) REVERT: C 601 ASP cc_start: 0.7022 (t0) cc_final: 0.6612 (t0) REVERT: D 107 PHE cc_start: 0.7824 (m-80) cc_final: 0.7600 (m-80) REVERT: D 286 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.5972 (pmm) REVERT: D 373 TYR cc_start: 0.7901 (t80) cc_final: 0.7505 (t80) REVERT: D 377 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7259 (p0) REVERT: D 601 ASP cc_start: 0.7035 (t0) cc_final: 0.6624 (t0) outliers start: 38 outliers final: 30 residues processed: 198 average time/residue: 0.2971 time to fit residues: 95.6443 Evaluate side-chains 206 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 0.0670 chunk 184 optimal weight: 2.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.184283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.159441 restraints weight = 21911.737| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.22 r_work: 0.3319 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.144 Angle : 0.471 7.919 29584 Z= 0.248 Chirality : 0.039 0.148 3404 Planarity : 0.002 0.026 3668 Dihedral : 3.818 22.635 2864 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.12 % Favored : 93.58 % Rotamer: Outliers : 1.76 % Allowed : 14.20 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2616 helix: 1.67 (0.15), residues: 1336 sheet: -1.41 (0.34), residues: 260 loop : -2.06 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 367 HIS 0.004 0.001 HIS D 570 PHE 0.012 0.001 PHE B 448 TYR 0.012 0.001 TYR B 460 ARG 0.004 0.000 ARG C 677 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.63 seconds wall clock time: 73 minutes 31.37 seconds (4411.37 seconds total)