Starting phenix.real_space_refine on Tue Apr 9 11:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnu_34918/04_2024/8hnu_34918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnu_34918/04_2024/8hnu_34918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnu_34918/04_2024/8hnu_34918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnu_34918/04_2024/8hnu_34918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnu_34918/04_2024/8hnu_34918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnu_34918/04_2024/8hnu_34918.pdb" } resolution = 2.28 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= 0.015 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 S 42 5.16 5 Cl 4 4.86 5 C 10156 2.51 5 N 2640 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 115": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 619": "OD1" <-> "OD2" Residue "B ASP 625": "OD1" <-> "OD2" Residue "B GLU 907": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16178 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7939 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} Conformer: "B" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} bond proxies already assigned to first conformer: 8000 Conformer: "C" Number of residues, atoms: 980, 7843 Classifications: {'peptide': 980} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 946} Chain breaks: 5 bond proxies already assigned to first conformer: 8000 Chain: "B" Number of atoms: 7919 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} Conformer: "B" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} bond proxies already assigned to first conformer: 8010 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Residues with excluded nonbonded symmetry interactions: 30 residue: pdb=" N ASP A 39 " occ=0.97 ... (6 atoms not shown) pdb=" OD2 ASP A 39 " occ=0.97 residue: pdb=" N ASER A 114 " occ=0.65 ... (10 atoms not shown) pdb=" OG BSER A 114 " occ=0.35 residue: pdb=" N GLU A 125 " occ=0.79 ... (7 atoms not shown) pdb=" OE2 GLU A 125 " occ=0.79 residue: pdb=" N ATHR A 157 " occ=0.66 ... (12 atoms not shown) pdb=" CG2BTHR A 157 " occ=0.34 residue: pdb=" N AARG A 171 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG A 171 " occ=0.48 residue: pdb=" N APHE A 296 " occ=0.36 ... (31 atoms not shown) pdb=" CZ CPHE A 296 " occ=0.39 residue: pdb=" N ATHR A 338 " occ=0.91 ... (12 atoms not shown) pdb=" CG2BTHR A 338 " occ=0.09 residue: pdb=" N GLU A 446 " occ=0.83 ... (7 atoms not shown) pdb=" OE2 GLU A 446 " occ=0.83 residue: pdb=" N ASP A 625 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 625 " occ=0.62 residue: pdb=" N ASER A 626 " occ=0.40 ... (10 atoms not shown) pdb=" OG BSER A 626 " occ=0.60 residue: pdb=" N GLU A 766 " occ=0.67 ... (7 atoms not shown) pdb=" OE2 GLU A 766 " occ=0.67 residue: pdb=" N ASP A 799 " occ=0.66 ... (6 atoms not shown) pdb=" OD2 ASP A 799 " occ=0.66 ... (remaining 18 not shown) Time building chain proxies: 19.71, per 1000 atoms: 1.22 Number of scatterers: 16178 At special positions: 0 Unit cell: (115.37, 131.14, 112.05, 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) Cl 4 17.00 S 42 16.00 O 3336 8.00 N 2640 7.00 C 10156 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: 6.26 Conformation dependent library (CDL) restraints added in 6.8 seconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 25 sheets defined 37.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.547A pdb=" N ASN A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.637A pdb=" N MET A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 removed outlier: 4.391A pdb=" N VAL A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 486 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 506 through 516 removed outlier: 5.669A pdb=" N TYR A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 559 through 573 removed outlier: 4.378A pdb=" N GLN A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.019A pdb=" N VAL A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 688 through 710 Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.822A pdb=" N PHE A 754 " --> pdb=" O PHE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.777A pdb=" N LYS A 795 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 836 through 853 removed outlier: 3.616A pdb=" N LEU A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 6.053A pdb=" N TYR A 857 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 890 through 904 removed outlier: 4.646A pdb=" N THR A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 115 through 119 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.574A pdb=" N THR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.537A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N APHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 434 removed outlier: 3.633A pdb=" N MET B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 455 removed outlier: 4.411A pdb=" N VAL B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 473 through 486 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 506 through 516 removed outlier: 5.671A pdb=" N TYR B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 559 through 573 removed outlier: 4.389A pdb=" N GLN B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.007A pdb=" N VAL B 577 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 635 through 651 Processing helix chain 'B' and resid 666 through 686 Processing helix chain 'B' and resid 688 through 710 Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.805A pdb=" N PHE B 754 " --> pdb=" O PHE B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.791A pdb=" N LYS B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 832 Processing helix chain 'B' and resid 836 through 853 removed outlier: 3.620A pdb=" N LEU B 853 " --> pdb=" O PHE B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 861 removed outlier: 6.045A pdb=" N TYR B 857 " --> pdb=" O VAL B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 890 through 904 removed outlier: 4.644A pdb=" N THR B 894 " --> pdb=" O SER B 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.380A pdb=" N GLN B 307 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 309 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 321 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 311 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 319 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 339 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG B 335 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR B 325 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N ASP B 333 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.380A pdb=" N GLN B 307 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 309 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 321 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 311 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 319 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 339 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG B 335 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR B 325 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N ASP B 333 " --> pdb=" O TYR B 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.299A pdb=" N VAL A 45 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N PHE A 82 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY A 47 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N GLU A 84 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.801A pdb=" N ARG A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.801A pdb=" N ARG A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N ASP A 333 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 325 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A 335 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 339 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 319 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 311 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 321 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 309 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN A 307 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 145 through 148 Processing sheet with id=AA7, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.421A pdb=" N LEU A 204 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR A 213 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A 202 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN A 201 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 460 removed outlier: 6.646A pdb=" N SER A 936 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 980 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS A 938 " --> pdb=" O VAL A 980 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 982 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER A 940 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE A 984 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 942 " --> pdb=" O PHE A 984 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.421A pdb=" N ASN A 541 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 543 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 712 removed outlier: 3.568A pdb=" N PHE A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 780 through 781 Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 816 Processing sheet with id=AB6, first strand: chain 'A' and resid 906 through 909 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 37 removed outlier: 3.808A pdb=" N PHE B 32 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 34 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA B 49 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 36 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLY B 47 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 45 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N PHE B 82 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 47 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLU B 84 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ALA B 49 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AB9, first strand: chain 'B' and resid 209 through 213 removed outlier: 6.423A pdb=" N LEU B 204 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR B 213 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE B 202 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 458 through 461 removed outlier: 3.603A pdb=" N ASN B 927 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER B 936 " --> pdb=" O HIS B 978 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL B 980 " --> pdb=" O SER B 936 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 938 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU B 982 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 940 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE B 984 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 942 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU B 957 " --> pdb=" O ILE B 964 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 499 through 500 removed outlier: 6.415A pdb=" N ASN B 541 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 543 " --> pdb=" O LYS B 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'B' and resid 664 through 665 Processing sheet with id=AC5, first strand: chain 'B' and resid 780 through 781 Processing sheet with id=AC6, first strand: chain 'B' and resid 815 through 816 Processing sheet with id=AC7, first strand: chain 'B' and resid 906 through 909 785 hydrogen bonds defined for protein. 2157 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: 7.12 Time building geometry restraints manager: 6.73 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: 5156 1.34 - 1.46: 3235 1.46 - 1.58: 7748 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 16223 Sorted by residual: bond pdb=" CA ASN A 588 " pdb=" CB ASN A 588 " ideal model delta sigma weight residual 1.533 1.550 -0.017 1.37e-02 5.33e+03 1.49e+00 bond pdb=" CB GLN A 87 " pdb=" CG GLN A 87 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.42e+00 bond pdb=" CB ASN A 588 " pdb=" CG ASN A 588 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.05e+00 bond pdb=" CB LYS B 648 " pdb=" CG LYS B 648 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.87e-01 ... (remaining 16218 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 356 106.99 - 113.74: 8812 113.74 - 120.50: 6318 120.50 - 127.25: 6362 127.25 - 134.01: 123 Bond angle restraints: 21971 Sorted by residual: angle pdb=" C LYS A 712 " pdb=" N GLU A 713 " pdb=" CA GLU A 713 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" C LYS B 712 " pdb=" N GLU B 713 " pdb=" CA GLU B 713 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" CB GLN A 87 " pdb=" CG GLN A 87 " pdb=" CD GLN A 87 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.70e+00 3.46e-01 8.82e+00 angle pdb=" CA ASN A 588 " pdb=" CB ASN A 588 " pdb=" CG ASN A 588 " ideal model delta sigma weight residual 112.60 115.49 -2.89 1.00e+00 1.00e+00 8.32e+00 angle pdb=" C THR B 407 " pdb=" N GLY B 408 " pdb=" CA GLY B 408 " ideal model delta sigma weight residual 120.91 116.99 3.92 1.38e+00 5.25e-01 8.06e+00 ... (remaining 21966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8561 17.93 - 35.86: 809 35.86 - 53.79: 223 53.79 - 71.72: 55 71.72 - 89.65: 22 Dihedral angle restraints: 9670 sinusoidal: 3870 harmonic: 5800 Sorted by residual: dihedral pdb=" CA LYS A 712 " pdb=" C LYS A 712 " pdb=" N GLU A 713 " pdb=" CA GLU A 713 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASP A 218 " pdb=" CB ASP A 218 " pdb=" CG ASP A 218 " pdb=" OD1 ASP A 218 " ideal model delta sinusoidal sigma weight residual -30.00 -88.24 58.24 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASN A 303 " pdb=" CB ASN A 303 " pdb=" CG ASN A 303 " pdb=" OD1 ASN A 303 " ideal model delta sinusoidal sigma weight residual -90.00 -162.14 72.14 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 9667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1340 0.027 - 0.055: 689 0.055 - 0.082: 210 0.082 - 0.109: 116 0.109 - 0.137: 45 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CA VAL A 166 " pdb=" N VAL A 166 " pdb=" C VAL A 166 " pdb=" CB VAL A 166 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE B 340 " pdb=" N ILE B 340 " pdb=" C ILE B 340 " pdb=" CB ILE B 340 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CB ILE B 775 " pdb=" CA ILE B 775 " pdb=" CG1 ILE B 775 " pdb=" CG2 ILE B 775 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 2397 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 588 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C ASN A 588 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 588 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 589 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 196 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 197 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 322 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 323 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.019 5.00e-02 4.00e+02 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 639 2.72 - 3.26: 15664 3.26 - 3.81: 28174 3.81 - 4.35: 37822 4.35 - 4.90: 60805 Nonbonded interactions: 143104 Sorted by model distance: nonbonded pdb=" N GLN A 690 " pdb=" OE1 GLN A 690 " model vdw 2.170 2.520 nonbonded pdb=" N GLN B 690 " pdb=" OE1 GLN B 690 " model vdw 2.171 2.520 nonbonded pdb=" O ASN A 588 " pdb=" ND2 ASN A 588 " model vdw 2.173 2.520 nonbonded pdb=" O MET B 537 " pdb=" O HOH B1101 " model vdw 2.243 2.440 nonbonded pdb=" O LEU A 260 " pdb=" O HOH A1101 " model vdw 2.258 2.440 ... (remaining 143099 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 2 through 113 or resid 115 through 156 or resid 158 throug \ h 170 or resid 172 through 295 or resid 297 through 337 or resid 339 through 343 \ or resid 345 through 625 or resid 627 through 785 or resid 787 through 986 or r \ esid 1001 through 1002)) selection = (chain 'B' and (resid 2 through 113 or resid 115 through 156 or resid 158 throug \ h 170 or resid 172 through 295 or resid 297 through 337 or resid 339 through 343 \ or resid 345 through 625 or resid 627 through 785 or resid 787 through 986 or r \ esid 1001 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.07 max=1.00 mean=0.99 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: 6.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.070 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 62.730 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 0.036 16223 Z= 0.185 Angle : 0.449 7.270 21971 Z= 0.250 Chirality : 0.041 0.137 2400 Planarity : 0.003 0.034 2853 Dihedral : 16.204 89.651 5960 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 1.52 % Allowed : 13.08 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 2002 helix: 1.69 (0.21), residues: 622 sheet: 0.95 (0.29), residues: 340 loop : 0.09 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 PHE 0.011 0.001 PHE B 928 TYR 0.012 0.001 TYR A 237 ARG 0.001 0.000 ARG B 810 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.868 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 22 residues processed: 112 average time/residue: 1.5483 time to fit residues: 191.4952 Evaluate side-chains 110 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 851 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 482 GLN B 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16223 Z= 0.267 Angle : 0.482 6.907 21971 Z= 0.271 Chirality : 0.043 0.140 2400 Planarity : 0.003 0.036 2853 Dihedral : 5.446 64.903 2207 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 0.93 % Allowed : 13.49 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2002 helix: 1.67 (0.21), residues: 626 sheet: 0.81 (0.29), residues: 342 loop : 0.07 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 756 HIS 0.005 0.001 HIS B 451 PHE 0.013 0.001 PHE B 928 TYR 0.014 0.001 TYR A 237 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 2.040 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 1.7478 time to fit residues: 191.7393 Evaluate side-chains 96 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 176 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN B 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16223 Z= 0.245 Angle : 0.475 6.745 21971 Z= 0.266 Chirality : 0.042 0.139 2400 Planarity : 0.003 0.037 2853 Dihedral : 4.544 54.126 2174 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.11 % Allowed : 13.31 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2002 helix: 1.62 (0.21), residues: 626 sheet: 0.80 (0.29), residues: 340 loop : 0.01 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 756 HIS 0.005 0.001 HIS B 451 PHE 0.014 0.001 PHE B 928 TYR 0.013 0.001 TYR A 237 ARG 0.001 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.928 Fit side-chains REVERT: B 264 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8829 (tt) REVERT: B 346 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5828 (pp20) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 1.5799 time to fit residues: 177.9708 Evaluate side-chains 98 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 0.0670 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 119 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16223 Z= 0.129 Angle : 0.429 6.450 21971 Z= 0.240 Chirality : 0.040 0.137 2400 Planarity : 0.003 0.036 2853 Dihedral : 4.085 52.218 2170 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.88 % Allowed : 13.95 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 2002 helix: 1.70 (0.21), residues: 638 sheet: 0.98 (0.29), residues: 336 loop : 0.02 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 756 HIS 0.002 0.000 HIS A 451 PHE 0.012 0.001 PHE B 928 TYR 0.010 0.001 TYR B 237 ARG 0.001 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.960 Fit side-chains REVERT: B 264 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8788 (tt) outliers start: 13 outliers final: 5 residues processed: 97 average time/residue: 1.6101 time to fit residues: 172.4419 Evaluate side-chains 94 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.6980 chunk 107 optimal weight: 0.0040 chunk 2 optimal weight: 0.0370 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 0.0270 chunk 130 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 461 ASN B 482 GLN B 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16223 Z= 0.118 Angle : 0.417 6.380 21971 Z= 0.232 Chirality : 0.040 0.134 2400 Planarity : 0.003 0.035 2853 Dihedral : 3.900 49.849 2170 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.76 % Allowed : 14.01 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 2002 helix: 1.85 (0.21), residues: 638 sheet: 1.06 (0.29), residues: 336 loop : 0.05 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 756 HIS 0.002 0.000 HIS B 451 PHE 0.011 0.001 PHE B 928 TYR 0.009 0.001 TYR A 237 ARG 0.001 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 2.146 Fit side-chains REVERT: B 264 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8770 (tt) outliers start: 11 outliers final: 4 residues processed: 105 average time/residue: 1.5331 time to fit residues: 178.4632 Evaluate side-chains 96 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16223 Z= 0.220 Angle : 0.465 6.350 21971 Z= 0.260 Chirality : 0.042 0.141 2400 Planarity : 0.003 0.035 2853 Dihedral : 4.021 20.737 2166 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.76 % Allowed : 14.24 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2002 helix: 1.68 (0.21), residues: 638 sheet: 0.97 (0.29), residues: 336 loop : 0.00 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 756 HIS 0.005 0.001 HIS A 451 PHE 0.014 0.001 PHE B 928 TYR 0.014 0.001 TYR A 237 ARG 0.001 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.857 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 1.6333 time to fit residues: 174.6995 Evaluate side-chains 92 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 605 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16223 Z= 0.238 Angle : 0.475 6.899 21971 Z= 0.266 Chirality : 0.042 0.138 2400 Planarity : 0.003 0.035 2853 Dihedral : 4.114 21.175 2166 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 14.36 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.95 (0.19), residues: 2002 helix: 1.64 (0.21), residues: 634 sheet: 0.91 (0.29), residues: 336 loop : -0.03 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 756 HIS 0.005 0.001 HIS B 451 PHE 0.014 0.001 PHE B 928 TYR 0.013 0.001 TYR A 237 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 2.036 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 1.6955 time to fit residues: 179.2437 Evaluate side-chains 95 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 482 GLN B 588 ASN B 859 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16223 Z= 0.338 Angle : 0.514 6.600 21971 Z= 0.288 Chirality : 0.044 0.144 2400 Planarity : 0.003 0.038 2853 Dihedral : 4.334 21.264 2166 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 0.76 % Allowed : 14.42 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.88 (0.19), residues: 2002 helix: 1.66 (0.21), residues: 618 sheet: 0.68 (0.29), residues: 342 loop : -0.04 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 756 HIS 0.006 0.001 HIS B 451 PHE 0.015 0.002 PHE B 928 TYR 0.016 0.002 TYR B 237 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.984 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 1.7684 time to fit residues: 190.4963 Evaluate side-chains 95 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 0.0270 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 166 optimal weight: 0.4980 chunk 175 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN B 859 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16223 Z= 0.164 Angle : 0.458 7.087 21971 Z= 0.256 Chirality : 0.041 0.136 2400 Planarity : 0.003 0.035 2853 Dihedral : 4.050 21.453 2166 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.58 % Allowed : 14.59 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.93 (0.19), residues: 2002 helix: 1.61 (0.21), residues: 634 sheet: 0.86 (0.29), residues: 338 loop : -0.03 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 756 HIS 0.004 0.000 HIS B 451 PHE 0.013 0.001 PHE B 928 TYR 0.010 0.001 TYR A 237 ARG 0.001 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 2.124 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 1.7484 time to fit residues: 177.4048 Evaluate side-chains 93 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 16223 Z= 0.242 Angle : 0.717 59.167 21971 Z= 0.436 Chirality : 0.050 1.358 2400 Planarity : 0.005 0.166 2853 Dihedral : 4.064 21.422 2166 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 0.70 % Allowed : 14.42 % Favored : 84.88 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.09 % 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: 0.93 (0.19), residues: 2002 helix: 1.57 (0.21), residues: 638 sheet: 0.86 (0.29), residues: 338 loop : -0.00 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 756 HIS 0.004 0.000 HIS B 451 PHE 0.013 0.001 PHE B 928 TYR 0.010 0.001 TYR A 237 ARG 0.001 0.000 ARG A 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 2.019 Fit side-chains REVERT: A 588 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8409 (t0) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 1.6143 time to fit residues: 167.7460 Evaluate side-chains 94 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 155 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.047869 restraints weight = 128882.572| |-----------------------------------------------------------------------------| r_work (start): 0.2473 rms_B_bonded: 4.06 r_work: 0.2284 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2295 r_free = 0.2295 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2294 r_free = 0.2294 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.422 16223 Z= 0.288 Angle : 0.698 48.974 21971 Z= 0.491 Chirality : 0.050 1.358 2400 Planarity : 0.005 0.166 2853 Dihedral : 4.064 21.422 2166 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 0.53 % Allowed : 14.48 % Favored : 85.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.09 % 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: 0.93 (0.19), residues: 2002 helix: 1.57 (0.21), residues: 638 sheet: 0.86 (0.29), residues: 338 loop : -0.00 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 756 HIS 0.004 0.000 HIS B 451 PHE 0.013 0.001 PHE B 928 TYR 0.010 0.001 TYR A 237 ARG 0.001 0.000 ARG A 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5139.45 seconds wall clock time: 93 minutes 55.24 seconds (5635.24 seconds total)