Starting phenix.real_space_refine on Wed Mar 4 06:55:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fd9_31537/03_2026/7fd9_31537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fd9_31537/03_2026/7fd9_31537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fd9_31537/03_2026/7fd9_31537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fd9_31537/03_2026/7fd9_31537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fd9_31537/03_2026/7fd9_31537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fd9_31537/03_2026/7fd9_31537.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 7384 2.51 5 N 1916 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 10, 'HIS:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 10, 'HIS:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.27, per 1000 atoms: 0.20 Number of scatterers: 11476 At special positions: 0 Unit cell: (79.21, 112.14, 178.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 2066 8.00 N 1916 7.00 C 7384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.04 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.04 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 594.7 milliseconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 51.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.664A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.570A pdb=" N SER A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.419A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.514A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.632A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.588A pdb=" N GLU A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.750A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.509A pdb=" N GLN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.564A pdb=" N MET A 429 " --> pdb=" O CYS A 426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 430' Processing helix chain 'A' and resid 433 through 443 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 577 through 604 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 636 removed outlier: 3.533A pdb=" N ILE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 3.914A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.692A pdb=" N ILE A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 760 Proline residue: A 743 - end of helix removed outlier: 3.985A pdb=" N LYS A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'A' and resid 770 through 794 Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 797 through 818 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.664A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.571A pdb=" N SER B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 4.419A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.515A pdb=" N LEU B 179 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.631A pdb=" N GLN B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.588A pdb=" N GLU B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.750A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.509A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.564A pdb=" N MET B 429 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 426 through 430' Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 577 through 604 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 636 removed outlier: 3.533A pdb=" N ILE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 3.913A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 692 through 715 removed outlier: 3.693A pdb=" N ILE B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 760 Proline residue: B 743 - end of helix removed outlier: 3.986A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 770 through 794 Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 797 through 818 Processing helix chain 'B' and resid 818 through 826 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.788A pdb=" N GLU A 94 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 96 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 41 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 36 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 146 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 38 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 8.075A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.818A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AA7, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.789A pdb=" N GLU B 94 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 96 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 41 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 36 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 146 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 38 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.076A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.819A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AB4, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AB5, first strand: chain 'B' and resid 720 through 722 596 hydrogen bonds defined for protein. 1722 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: 1.91 Time building geometry restraints manager: 1.24 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: 3604 1.34 - 1.47: 2964 1.47 - 1.59: 5018 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 11742 Sorted by residual: bond pdb=" CAS Z99 A 902 " pdb=" CAU Z99 A 902 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CAS Z99 B 902 " pdb=" CAU Z99 B 902 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CAT Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C CYS B 419 " pdb=" N PRO B 420 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.10e+01 ... (remaining 11737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 15951 4.37 - 8.74: 37 8.74 - 13.11: 12 13.11 - 17.49: 2 17.49 - 21.86: 2 Bond angle restraints: 16004 Sorted by residual: angle pdb=" CAN Z99 A 902 " pdb=" CAW Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 108.20 130.06 -21.86 3.00e+00 1.11e-01 5.31e+01 angle pdb=" CAN Z99 B 902 " pdb=" CAW Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 108.20 130.05 -21.85 3.00e+00 1.11e-01 5.30e+01 angle pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAY Z99 B 902 " ideal model delta sigma weight residual 117.71 131.39 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAY Z99 A 902 " ideal model delta sigma weight residual 117.71 131.35 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " pdb=" CAW Z99 A 902 " ideal model delta sigma weight residual 118.77 106.06 12.71 3.00e+00 1.11e-01 1.80e+01 ... (remaining 15999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 6886 34.06 - 68.11: 102 68.11 - 102.17: 22 102.17 - 136.23: 6 136.23 - 170.28: 18 Dihedral angle restraints: 7034 sinusoidal: 2574 harmonic: 4460 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.80 78.80 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.77 78.77 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 155.70 -62.70 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 7031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.536: 1844 0.536 - 1.072: 2 1.072 - 1.607: 0 1.607 - 2.143: 0 2.143 - 2.679: 2 Chirality restraints: 1848 Sorted by residual: chirality pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAU Z99 B 902 " pdb=" CAV Z99 B 902 " both_signs ideal model delta sigma weight residual False 2.61 -0.07 2.68 2.00e-01 2.50e+01 1.79e+02 chirality pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAU Z99 A 902 " pdb=" CAV Z99 A 902 " both_signs ideal model delta sigma weight residual False 2.61 -0.06 2.67 2.00e-01 2.50e+01 1.79e+02 chirality pdb=" CAY Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAR Z99 B 902 " pdb=" CAZ Z99 B 902 " both_signs ideal model delta sigma weight residual False -2.97 -2.38 -0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 1845 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAG Z99 A 902 " 0.016 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CAI Z99 A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 A 902 " 0.006 2.00e-02 2.50e+03 pdb=" CAM Z99 A 902 " -0.023 2.00e-02 2.50e+03 pdb=" CAT Z99 A 902 " 0.002 2.00e-02 2.50e+03 pdb=" CAV Z99 A 902 " -0.035 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.043 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAG Z99 B 902 " 0.016 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CAI Z99 B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 B 902 " 0.005 2.00e-02 2.50e+03 pdb=" CAM Z99 B 902 " -0.022 2.00e-02 2.50e+03 pdb=" CAT Z99 B 902 " 0.003 2.00e-02 2.50e+03 pdb=" CAV Z99 B 902 " -0.034 2.00e-02 2.50e+03 pdb=" CAW Z99 B 902 " 0.042 2.00e-02 2.50e+03 pdb=" OAP Z99 B 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAF Z99 A 902 " 0.000 2.00e-02 2.50e+03 1.22e-02 3.00e+00 pdb=" CAH Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAJ Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAL Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" CAS Z99 A 902 " 0.007 2.00e-02 2.50e+03 pdb=" CAU Z99 A 902 " -0.030 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1877 2.79 - 3.32: 12074 3.32 - 3.85: 19082 3.85 - 4.37: 20764 4.37 - 4.90: 35950 Nonbonded interactions: 89747 Sorted by model distance: nonbonded pdb=" OE1 GLN A 198 " pdb=" OG SER A 304 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLN B 198 " pdb=" OG SER B 304 " model vdw 2.266 3.040 nonbonded pdb=" O SER A 116 " pdb=" OG SER A 119 " model vdw 2.288 3.040 nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.288 3.040 nonbonded pdb=" NH2 ARG B 648 " pdb=" OD1 ASN B 734 " model vdw 2.320 3.120 ... (remaining 89742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.920 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11764 Z= 0.464 Angle : 1.313 21.858 16050 Z= 0.844 Chirality : 0.127 2.679 1848 Planarity : 0.003 0.023 2026 Dihedral : 17.544 170.285 4110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1522 helix: 0.96 (0.19), residues: 700 sheet: -0.60 (0.47), residues: 124 loop : -2.22 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 351 TYR 0.012 0.002 TYR A 645 PHE 0.013 0.003 PHE B 165 TRP 0.013 0.002 TRP B 532 HIS 0.004 0.002 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00703 (11742) covalent geometry : angle 1.28268 (16004) SS BOND : bond 0.00751 ( 20) SS BOND : angle 1.44731 ( 40) hydrogen bonds : bond 0.12546 ( 596) hydrogen bonds : angle 5.66462 ( 1722) link_NAG-ASN : bond 0.02961 ( 2) link_NAG-ASN : angle 14.36925 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 414 MET cc_start: 0.8629 (tmm) cc_final: 0.8350 (tmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0719 time to fit residues: 9.1940 Evaluate side-chains 60 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.072740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052476 restraints weight = 74023.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053757 restraints weight = 38251.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054616 restraints weight = 24558.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.055166 restraints weight = 18260.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055378 restraints weight = 14907.685| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11764 Z= 0.122 Angle : 0.590 12.254 16050 Z= 0.290 Chirality : 0.043 0.207 1848 Planarity : 0.003 0.027 2026 Dihedral : 13.626 119.893 1742 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.71 % Allowed : 6.71 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1522 helix: 1.26 (0.19), residues: 726 sheet: -0.68 (0.43), residues: 134 loop : -1.92 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.020 0.001 TYR A 340 PHE 0.018 0.001 PHE B 277 TRP 0.013 0.001 TRP A 500 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00257 (11742) covalent geometry : angle 0.56904 (16004) SS BOND : bond 0.00212 ( 20) SS BOND : angle 0.82911 ( 40) hydrogen bonds : bond 0.04352 ( 596) hydrogen bonds : angle 4.53710 ( 1722) link_NAG-ASN : bond 0.01779 ( 2) link_NAG-ASN : angle 8.01590 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9024 (tmm) cc_final: 0.8680 (tmm) REVERT: B 290 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8160 (mmm) REVERT: B 414 MET cc_start: 0.9079 (tmm) cc_final: 0.8446 (tmm) outliers start: 8 outliers final: 0 residues processed: 66 average time/residue: 0.0789 time to fit residues: 8.6950 Evaluate side-chains 62 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 54 optimal weight: 50.0000 chunk 126 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 74 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.068989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.048245 restraints weight = 72251.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.048633 restraints weight = 43981.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.049214 restraints weight = 29258.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.049322 restraints weight = 21604.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049478 restraints weight = 20710.770| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11764 Z= 0.285 Angle : 0.675 11.516 16050 Z= 0.338 Chirality : 0.044 0.255 1848 Planarity : 0.004 0.028 2026 Dihedral : 10.217 125.905 1742 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.06 % Allowed : 8.75 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1522 helix: 1.20 (0.19), residues: 720 sheet: -0.88 (0.42), residues: 138 loop : -2.05 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 200 TYR 0.029 0.002 TYR A 340 PHE 0.018 0.001 PHE A 277 TRP 0.012 0.002 TRP B 359 HIS 0.005 0.002 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00607 (11742) covalent geometry : angle 0.65760 (16004) SS BOND : bond 0.00451 ( 20) SS BOND : angle 1.11286 ( 40) hydrogen bonds : bond 0.04264 ( 596) hydrogen bonds : angle 4.59930 ( 1722) link_NAG-ASN : bond 0.01590 ( 2) link_NAG-ASN : angle 7.51745 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9040 (ttp) REVERT: A 277 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: A 301 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9438 (mm) REVERT: A 414 MET cc_start: 0.9153 (tmm) cc_final: 0.8937 (tmm) REVERT: A 768 PHE cc_start: 0.5929 (m-80) cc_final: 0.5709 (t80) REVERT: B 202 MET cc_start: 0.9046 (mtt) cc_final: 0.8798 (mtt) REVERT: B 277 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: B 290 MET cc_start: 0.8545 (mmp) cc_final: 0.8109 (mmm) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 0.0789 time to fit residues: 9.0847 Evaluate side-chains 66 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 64 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 19 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 overall best weight: 5.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.069752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048751 restraints weight = 73674.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050030 restraints weight = 37710.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.050854 restraints weight = 24305.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.051349 restraints weight = 18180.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051607 restraints weight = 15034.533| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11764 Z= 0.279 Angle : 0.652 11.604 16050 Z= 0.329 Chirality : 0.044 0.226 1848 Planarity : 0.004 0.029 2026 Dihedral : 9.491 134.402 1742 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.47 % Allowed : 9.01 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1522 helix: 1.12 (0.19), residues: 720 sheet: -0.96 (0.43), residues: 148 loop : -1.91 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 200 TYR 0.030 0.002 TYR B 340 PHE 0.015 0.002 PHE B 188 TRP 0.014 0.002 TRP B 359 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00595 (11742) covalent geometry : angle 0.63558 (16004) SS BOND : bond 0.00258 ( 20) SS BOND : angle 1.03548 ( 40) hydrogen bonds : bond 0.04155 ( 596) hydrogen bonds : angle 4.60072 ( 1722) link_NAG-ASN : bond 0.01731 ( 2) link_NAG-ASN : angle 7.22174 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9154 (tmm) cc_final: 0.8844 (tmm) REVERT: A 444 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (t) REVERT: B 72 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8976 (ttp) REVERT: B 277 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: B 290 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: B 405 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: B 414 MET cc_start: 0.9000 (tmm) cc_final: 0.8665 (tmm) outliers start: 28 outliers final: 11 residues processed: 80 average time/residue: 0.0821 time to fit residues: 10.5699 Evaluate side-chains 74 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN B 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.070661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049272 restraints weight = 69900.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050568 restraints weight = 35975.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051438 restraints weight = 23223.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051989 restraints weight = 17294.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052264 restraints weight = 14352.036| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11764 Z= 0.118 Angle : 0.551 11.458 16050 Z= 0.274 Chirality : 0.042 0.181 1848 Planarity : 0.003 0.030 2026 Dihedral : 9.211 134.244 1742 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.33 % Allowed : 10.51 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1522 helix: 1.34 (0.19), residues: 732 sheet: -0.65 (0.44), residues: 138 loop : -1.83 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 26 TYR 0.014 0.001 TYR B 340 PHE 0.016 0.001 PHE A 277 TRP 0.017 0.001 TRP B 500 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00247 (11742) covalent geometry : angle 0.53213 (16004) SS BOND : bond 0.00215 ( 20) SS BOND : angle 0.84772 ( 40) hydrogen bonds : bond 0.03798 ( 596) hydrogen bonds : angle 4.27792 ( 1722) link_NAG-ASN : bond 0.01748 ( 2) link_NAG-ASN : angle 7.18159 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: A 405 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 72 MET cc_start: 0.9263 (ttp) cc_final: 0.8954 (ttp) REVERT: B 277 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: B 290 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8173 (mmm) REVERT: B 405 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7887 (m-10) REVERT: B 414 MET cc_start: 0.9029 (tmm) cc_final: 0.8824 (tmm) outliers start: 15 outliers final: 5 residues processed: 69 average time/residue: 0.0784 time to fit residues: 9.0059 Evaluate side-chains 68 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 0.0030 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.070878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.050528 restraints weight = 72709.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051970 restraints weight = 40540.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.052399 restraints weight = 23551.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052433 restraints weight = 21497.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052518 restraints weight = 19014.749| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11764 Z= 0.159 Angle : 0.570 10.919 16050 Z= 0.282 Chirality : 0.042 0.166 1848 Planarity : 0.003 0.030 2026 Dihedral : 9.035 135.409 1742 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.12 % Allowed : 9.89 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1522 helix: 1.39 (0.19), residues: 732 sheet: -0.60 (0.44), residues: 138 loop : -1.78 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 26 TYR 0.017 0.001 TYR A 340 PHE 0.008 0.001 PHE B 363 TRP 0.015 0.002 TRP B 557 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00340 (11742) covalent geometry : angle 0.55294 (16004) SS BOND : bond 0.00187 ( 20) SS BOND : angle 0.84378 ( 40) hydrogen bonds : bond 0.03760 ( 596) hydrogen bonds : angle 4.25467 ( 1722) link_NAG-ASN : bond 0.01476 ( 2) link_NAG-ASN : angle 7.03450 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: A 405 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: B 72 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8957 (ttp) REVERT: B 277 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: B 290 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8210 (mmm) REVERT: B 405 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7908 (m-10) outliers start: 24 outliers final: 11 residues processed: 75 average time/residue: 0.0895 time to fit residues: 10.5302 Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 30.0000 chunk 131 optimal weight: 40.0000 chunk 138 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.068608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046941 restraints weight = 71565.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.048207 restraints weight = 37832.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049079 restraints weight = 24819.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.049593 restraints weight = 18757.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049936 restraints weight = 15635.883| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11764 Z= 0.296 Angle : 0.688 10.331 16050 Z= 0.341 Chirality : 0.044 0.212 1848 Planarity : 0.004 0.031 2026 Dihedral : 9.157 136.967 1742 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.47 % Allowed : 10.25 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1522 helix: 1.22 (0.19), residues: 720 sheet: -0.80 (0.43), residues: 148 loop : -1.81 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 26 TYR 0.023 0.002 TYR B 340 PHE 0.012 0.001 PHE B 363 TRP 0.021 0.002 TRP A 557 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00627 (11742) covalent geometry : angle 0.67333 (16004) SS BOND : bond 0.00263 ( 20) SS BOND : angle 1.00782 ( 40) hydrogen bonds : bond 0.04089 ( 596) hydrogen bonds : angle 4.50497 ( 1722) link_NAG-ASN : bond 0.01052 ( 2) link_NAG-ASN : angle 6.98087 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: A 290 MET cc_start: 0.8862 (mmm) cc_final: 0.8607 (mmp) REVERT: A 405 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: B 277 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: B 290 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: B 405 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8066 (m-10) REVERT: B 414 MET cc_start: 0.9087 (tmm) cc_final: 0.8554 (tmm) REVERT: B 429 MET cc_start: 0.8495 (ttm) cc_final: 0.7993 (tpp) outliers start: 28 outliers final: 18 residues processed: 81 average time/residue: 0.0827 time to fit residues: 10.6278 Evaluate side-chains 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.070413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049084 restraints weight = 71242.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050334 restraints weight = 36372.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051198 restraints weight = 23445.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051699 restraints weight = 17572.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052062 restraints weight = 14617.596| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11764 Z= 0.121 Angle : 0.577 10.524 16050 Z= 0.280 Chirality : 0.041 0.197 1848 Planarity : 0.003 0.029 2026 Dihedral : 9.008 136.288 1742 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.12 % Allowed : 11.13 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1522 helix: 1.37 (0.19), residues: 732 sheet: -0.59 (0.44), residues: 138 loop : -1.73 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.012 0.001 TYR A 340 PHE 0.007 0.001 PHE A 277 TRP 0.012 0.001 TRP A 557 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00260 (11742) covalent geometry : angle 0.56215 (16004) SS BOND : bond 0.00188 ( 20) SS BOND : angle 0.78433 ( 40) hydrogen bonds : bond 0.03710 ( 596) hydrogen bonds : angle 4.20988 ( 1722) link_NAG-ASN : bond 0.01409 ( 2) link_NAG-ASN : angle 6.66953 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.8694 (tpp) cc_final: 0.8254 (mmp) REVERT: A 277 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: A 405 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: B 228 MET cc_start: 0.8638 (tpp) cc_final: 0.8196 (mmp) REVERT: B 277 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: B 290 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8165 (mmm) REVERT: B 405 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7856 (m-10) REVERT: B 414 MET cc_start: 0.9083 (tmm) cc_final: 0.8661 (tmm) outliers start: 24 outliers final: 14 residues processed: 80 average time/residue: 0.0864 time to fit residues: 10.8856 Evaluate side-chains 80 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.070178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.048588 restraints weight = 69872.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049837 restraints weight = 36135.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050674 restraints weight = 23516.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051193 restraints weight = 17819.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051456 restraints weight = 14829.451| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11764 Z= 0.125 Angle : 0.581 11.146 16050 Z= 0.279 Chirality : 0.041 0.196 1848 Planarity : 0.003 0.030 2026 Dihedral : 8.818 136.606 1742 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.94 % Allowed : 11.48 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.22), residues: 1522 helix: 1.52 (0.19), residues: 724 sheet: -0.44 (0.44), residues: 138 loop : -1.66 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 26 TYR 0.013 0.001 TYR B 340 PHE 0.014 0.001 PHE A 358 TRP 0.011 0.001 TRP A 557 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00270 (11742) covalent geometry : angle 0.56718 (16004) SS BOND : bond 0.00156 ( 20) SS BOND : angle 0.79659 ( 40) hydrogen bonds : bond 0.03636 ( 596) hydrogen bonds : angle 4.17723 ( 1722) link_NAG-ASN : bond 0.01273 ( 2) link_NAG-ASN : angle 6.48293 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: B 290 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: B 405 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7841 (m-10) REVERT: B 414 MET cc_start: 0.9036 (tmm) cc_final: 0.8535 (tmm) outliers start: 22 outliers final: 16 residues processed: 80 average time/residue: 0.0867 time to fit residues: 11.0126 Evaluate side-chains 82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 53 optimal weight: 5.9990 chunk 106 optimal weight: 0.0770 chunk 54 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 125 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.068779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.047087 restraints weight = 70216.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048070 restraints weight = 37001.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049106 restraints weight = 25482.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049639 restraints weight = 18819.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.049978 restraints weight = 15670.243| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11764 Z= 0.236 Angle : 0.662 12.673 16050 Z= 0.321 Chirality : 0.042 0.212 1848 Planarity : 0.003 0.029 2026 Dihedral : 8.862 138.061 1742 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.77 % Allowed : 11.66 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1522 helix: 1.32 (0.19), residues: 730 sheet: -0.47 (0.43), residues: 148 loop : -1.72 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.021 0.001 TYR B 340 PHE 0.015 0.001 PHE B 358 TRP 0.016 0.002 TRP A 359 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00506 (11742) covalent geometry : angle 0.64904 (16004) SS BOND : bond 0.00235 ( 20) SS BOND : angle 0.94012 ( 40) hydrogen bonds : bond 0.03834 ( 596) hydrogen bonds : angle 4.35117 ( 1722) link_NAG-ASN : bond 0.00951 ( 2) link_NAG-ASN : angle 6.42140 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 290 MET cc_start: 0.8503 (mmp) cc_final: 0.8163 (mmm) REVERT: B 405 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7987 (m-10) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.0887 time to fit residues: 11.1150 Evaluate side-chains 80 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 727 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 704 GLN Chi-restraints excluded: chain B residue 727 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.069228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047614 restraints weight = 70255.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.048866 restraints weight = 36403.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049696 restraints weight = 23756.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050221 restraints weight = 18003.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050567 restraints weight = 14964.026| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11764 Z= 0.189 Angle : 0.628 13.067 16050 Z= 0.304 Chirality : 0.042 0.207 1848 Planarity : 0.003 0.030 2026 Dihedral : 8.851 138.453 1742 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.77 % Allowed : 11.57 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1522 helix: 1.42 (0.19), residues: 718 sheet: -0.42 (0.43), residues: 148 loop : -1.69 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.018 0.001 TYR B 340 PHE 0.013 0.001 PHE B 358 TRP 0.013 0.002 TRP B 359 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00408 (11742) covalent geometry : angle 0.61555 (16004) SS BOND : bond 0.00183 ( 20) SS BOND : angle 0.97950 ( 40) hydrogen bonds : bond 0.03755 ( 596) hydrogen bonds : angle 4.29438 ( 1722) link_NAG-ASN : bond 0.01042 ( 2) link_NAG-ASN : angle 6.19375 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.00 seconds wall clock time: 33 minutes 47.42 seconds (2027.42 seconds total)