Starting phenix.real_space_refine on Fri Jul 3 02:41:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fd9_31537/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.map" model { file = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fd9_31537/07_2026/7fd9_31537.cif" } 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-6108/lib/python3.11/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 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 chiralities: 1 Time building chain proxies: 2.02, per 1000 atoms: 0.18 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: 0.92 Conformation dependent library (CDL) restraints added in 582.3 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: 0.34 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: 2.00 Time building geometry restraints manager: 1.25 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 - 15.77: 6341 15.77 - 31.53: 487 31.53 - 47.30: 96 47.30 - 63.06: 16 63.06 - 78.83: 10 Dihedral angle restraints: 6950 sinusoidal: 2490 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 6947 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: 0.03 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 11.806 78.828 4026 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/Z covalent geometry : bond 0.00703 / 0.46 (11742) covalent geometry : angle 1.28268 / 0.84 (16004) SS BOND : bond 0.00751 / 0.51 ( 20) SS BOND : angle 1.44731 / 1.03 ( 40) hydrogen bonds : bond 0.12546 / 8.63 ( 596) hydrogen bonds : angle 5.66462 / 3.94 ( 1722) link_NAG-ASN : bond 0.02961 / 1.49 ( 2) link_NAG-ASN : angle 14.36925 / 7.96 ( 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 : 0.427 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: 0.0784 time to fit residues: 9.9614 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 : 0.438 ------------------------------------------------------------------------------- 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... A 74 HIS ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.072730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052489 restraints weight = 74056.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053738 restraints weight = 38228.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.054581 restraints weight = 24619.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055110 restraints weight = 18290.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055388 restraints weight = 15015.525| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11764 Z= 0.120 Angle : 0.573 11.917 16050 Z= 0.285 Chirality : 0.043 0.266 1848 Planarity : 0.003 0.027 2026 Dihedral : 5.844 70.075 1658 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.71 % Allowed : 6.63 % Favored : 92.67 % 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 (0.44), 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 0.023 0.001 TYR A 340 PHE 0.015 0.001 PHE B 277 TRP 0.013 0.001 TRP B 500 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (11742) covalent geometry : angle 0.55300 / 0.28 (16004) SS BOND : bond 0.00185 / 0.14 ( 20) SS BOND : angle 0.84623 / 0.62 ( 40) hydrogen bonds : bond 0.04333 / 2.93 ( 596) hydrogen bonds : angle 4.50675 / 3.16 ( 1722) link_NAG-ASN : bond 0.01802 / 0.90 ( 2) link_NAG-ASN : angle 7.67532 / 3.80 ( 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 : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9015 (tmm) cc_final: 0.8667 (tmm) REVERT: B 290 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: B 414 MET cc_start: 0.9070 (tmm) cc_final: 0.8436 (tmm) outliers start: 8 outliers final: 0 residues processed: 67 average time/residue: 0.0738 time to fit residues: 8.2387 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 : 0.450 ------------------------------------------------------------------------------- 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: 30.0000 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 54 optimal weight: 50.0000 chunk 126 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.068456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046739 restraints weight = 72538.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.047975 restraints weight = 38335.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.048794 restraints weight = 25291.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049353 restraints weight = 19210.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.049681 restraints weight = 15987.366| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 11764 Z= 0.326 Angle : 0.717 10.760 16050 Z= 0.362 Chirality : 0.046 0.224 1848 Planarity : 0.004 0.029 2026 Dihedral : 5.819 67.111 1658 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.50 % Allowed : 8.39 % Favored : 90.11 % 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: -0.65 (0.21), residues: 1522 helix: 1.05 (0.19), residues: 722 sheet: -1.01 (0.42), residues: 138 loop : -2.05 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.029 0.002 TYR A 340 PHE 0.023 0.002 PHE A 277 TRP 0.014 0.002 TRP B 359 HIS 0.007 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.33 (11742) covalent geometry : angle 0.69900 / 0.36 (16004) SS BOND : bond 0.00447 / 0.32 ( 20) SS BOND : angle 1.22389 / 0.93 ( 40) hydrogen bonds : bond 0.04483 / 3.03 ( 596) hydrogen bonds : angle 4.71524 / 3.32 ( 1722) link_NAG-ASN : bond 0.01274 / 0.64 ( 2) link_NAG-ASN : angle 7.77567 / 3.95 ( 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 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9114 (tmm) cc_final: 0.8760 (tmm) REVERT: A 768 PHE cc_start: 0.5991 (m-80) cc_final: 0.5714 (t80) REVERT: B 277 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: B 290 MET cc_start: 0.8480 (mmp) cc_final: 0.8048 (mmm) outliers start: 17 outliers final: 6 residues processed: 73 average time/residue: 0.0755 time to fit residues: 9.2199 Evaluate side-chains 65 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 B residue 27 VAL Chi-restraints excluded: chain B residue 205 ILE 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: 10.0000 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 64 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 88 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.069788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.048226 restraints weight = 72121.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049505 restraints weight = 37663.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050363 restraints weight = 24659.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050932 restraints weight = 18472.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051294 restraints weight = 15273.034| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11764 Z= 0.176 Angle : 0.593 11.364 16050 Z= 0.295 Chirality : 0.042 0.185 1848 Planarity : 0.003 0.030 2026 Dihedral : 5.598 66.084 1658 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.86 % Allowed : 8.92 % Favored : 89.22 % 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: -0.41 (0.21), residues: 1522 helix: 1.27 (0.19), residues: 720 sheet: -0.91 (0.41), residues: 148 loop : -1.94 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 26 TYR 0.022 0.001 TYR B 340 PHE 0.016 0.001 PHE A 277 TRP 0.017 0.002 TRP A 500 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (11742) covalent geometry : angle 0.57405 / 0.29 (16004) SS BOND : bond 0.00247 / 0.18 ( 20) SS BOND : angle 0.93338 / 0.70 ( 40) hydrogen bonds : bond 0.03957 / 2.67 ( 596) hydrogen bonds : angle 4.43117 / 3.12 ( 1722) link_NAG-ASN : bond 0.01517 / 0.76 ( 2) link_NAG-ASN : angle 7.38900 / 3.68 ( 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 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 405 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: A 414 MET cc_start: 0.9103 (tmm) cc_final: 0.8803 (tmm) REVERT: A 444 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 72 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8963 (ttp) REVERT: B 202 MET cc_start: 0.8969 (mtt) cc_final: 0.8655 (mtt) REVERT: B 277 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: B 290 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: B 405 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7994 (m-10) REVERT: B 414 MET cc_start: 0.8974 (tmm) cc_final: 0.8631 (tmm) outliers start: 21 outliers final: 7 residues processed: 76 average time/residue: 0.0789 time to fit residues: 10.0140 Evaluate side-chains 73 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 117 LEU 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 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 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 704 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 34 optimal weight: 0.0040 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.071981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.051198 restraints weight = 73407.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052492 restraints weight = 38324.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.053341 restraints weight = 24887.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053853 restraints weight = 18590.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054158 restraints weight = 15342.475| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11764 Z= 0.102 Angle : 0.548 11.198 16050 Z= 0.269 Chirality : 0.042 0.179 1848 Planarity : 0.003 0.030 2026 Dihedral : 5.282 64.743 1658 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.24 % Allowed : 9.89 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.21), residues: 1522 helix: 1.41 (0.19), residues: 732 sheet: -0.63 (0.43), residues: 138 loop : -1.90 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.016 0.001 TYR A 340 PHE 0.009 0.001 PHE A 277 TRP 0.013 0.001 TRP A 500 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (11742) covalent geometry : angle 0.52865 / 0.26 (16004) SS BOND : bond 0.00222 / 0.15 ( 20) SS BOND : angle 0.79843 / 0.58 ( 40) hydrogen bonds : bond 0.03752 / 2.53 ( 596) hydrogen bonds : angle 4.23261 / 2.99 ( 1722) link_NAG-ASN : bond 0.01626 / 0.82 ( 2) link_NAG-ASN : angle 7.31702 / 3.65 ( 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: 14 poor density : 61 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 405 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: B 72 MET cc_start: 0.9246 (ttp) cc_final: 0.8936 (ttp) REVERT: B 202 MET cc_start: 0.8866 (mtt) cc_final: 0.8520 (mtt) REVERT: B 277 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: B 290 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: B 405 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: B 414 MET cc_start: 0.8997 (tmm) cc_final: 0.8618 (tmm) outliers start: 14 outliers final: 7 residues processed: 69 average time/residue: 0.0885 time to fit residues: 9.9143 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 117 LEU 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 609 VAL 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: 0.0370 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.070305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048872 restraints weight = 70286.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050169 restraints weight = 36414.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051028 restraints weight = 23669.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051558 restraints weight = 17798.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051843 restraints weight = 14715.485| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11764 Z= 0.156 Angle : 0.571 10.852 16050 Z= 0.280 Chirality : 0.042 0.170 1848 Planarity : 0.003 0.030 2026 Dihedral : 5.170 63.206 1658 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.86 % Allowed : 9.63 % 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: -0.13 (0.21), residues: 1522 helix: 1.45 (0.19), residues: 732 sheet: -0.53 (0.44), residues: 138 loop : -1.84 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 26 TYR 0.016 0.001 TYR A 340 PHE 0.008 0.001 PHE A 277 TRP 0.009 0.001 TRP B 359 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (11742) covalent geometry : angle 0.55351 / 0.28 (16004) SS BOND : bond 0.00181 / 0.13 ( 20) SS BOND : angle 0.81727 / 0.61 ( 40) hydrogen bonds : bond 0.03722 / 2.50 ( 596) hydrogen bonds : angle 4.23437 / 2.98 ( 1722) link_NAG-ASN : bond 0.01324 / 0.66 ( 2) link_NAG-ASN : angle 7.16716 / 3.60 ( 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 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 405 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: B 72 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8989 (ttp) REVERT: B 277 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: B 290 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: B 405 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8002 (m-10) outliers start: 21 outliers final: 11 residues processed: 75 average time/residue: 0.0730 time to fit residues: 9.1524 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 117 LEU 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 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 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 609 VAL Chi-restraints excluded: chain B residue 704 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 40.0000 chunk 131 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3643 r_free = 0.3643 target = 0.067556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046123 restraints weight = 71806.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.047590 restraints weight = 41990.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047912 restraints weight = 23741.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048127 restraints weight = 21174.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048144 restraints weight = 19630.655| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 11764 Z= 0.428 Angle : 0.826 10.363 16050 Z= 0.412 Chirality : 0.047 0.210 1848 Planarity : 0.004 0.031 2026 Dihedral : 5.718 63.952 1658 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.47 % Allowed : 10.34 % Favored : 87.19 % 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: -0.62 (0.21), residues: 1522 helix: 0.98 (0.19), residues: 720 sheet: -1.02 (0.44), residues: 138 loop : -1.89 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.033 0.002 TYR B 340 PHE 0.017 0.002 PHE A 277 TRP 0.025 0.003 TRP A 557 HIS 0.008 0.002 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00903 / 0.43 (11742) covalent geometry : angle 0.81360 / 0.41 (16004) SS BOND : bond 0.00371 / 0.28 ( 20) SS BOND : angle 1.16703 / 0.89 ( 40) hydrogen bonds : bond 0.04544 / 3.07 ( 596) hydrogen bonds : angle 4.85513 / 3.43 ( 1722) link_NAG-ASN : bond 0.00790 / 0.40 ( 2) link_NAG-ASN : angle 7.10361 / 3.61 ( 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 86 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: A 405 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: A 444 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8719 (t) REVERT: B 277 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: B 290 MET cc_start: 0.8499 (mmp) cc_final: 0.8087 (mmm) REVERT: B 405 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8265 (m-80) outliers start: 28 outliers final: 13 residues processed: 79 average time/residue: 0.0884 time to fit residues: 11.0631 Evaluate side-chains 76 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 146 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 444 THR 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 277 PHE 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 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: 10.0000 chunk 84 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 19 optimal weight: 0.0770 chunk 115 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.069750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047970 restraints weight = 70107.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049196 restraints weight = 36237.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050071 restraints weight = 23707.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.050602 restraints weight = 17942.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050885 restraints weight = 14915.639| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11764 Z= 0.135 Angle : 0.619 10.794 16050 Z= 0.298 Chirality : 0.042 0.175 1848 Planarity : 0.003 0.030 2026 Dihedral : 5.404 64.167 1658 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -0.28 (0.21), residues: 1522 helix: 1.33 (0.19), residues: 720 sheet: -0.74 (0.43), residues: 148 loop : -1.84 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.015 0.001 TYR B 340 PHE 0.009 0.001 PHE A 277 TRP 0.021 0.002 TRP B 557 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11742) covalent geometry : angle 0.60387 / 0.29 (16004) SS BOND : bond 0.00202 / 0.15 ( 20) SS BOND : angle 0.74720 / 0.55 ( 40) hydrogen bonds : bond 0.03901 / 2.64 ( 596) hydrogen bonds : angle 4.34294 / 3.06 ( 1722) link_NAG-ASN : bond 0.01585 / 0.79 ( 2) link_NAG-ASN : angle 6.89195 / 3.42 ( 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 83 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8681 (tpp) cc_final: 0.8233 (mmp) REVERT: A 277 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: A 405 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7867 (m-10) REVERT: A 414 MET cc_start: 0.9046 (tmm) cc_final: 0.8830 (tmm) REVERT: A 444 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8683 (t) REVERT: B 277 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: B 290 MET cc_start: 0.8468 (mmp) cc_final: 0.8142 (mmm) REVERT: B 405 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: B 414 MET cc_start: 0.9106 (tmm) cc_final: 0.8497 (tmm) REVERT: B 429 MET cc_start: 0.8315 (ttm) cc_final: 0.7926 (tpp) outliers start: 22 outliers final: 12 residues processed: 78 average time/residue: 0.0778 time to fit residues: 9.6626 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 : 0.339 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 444 THR 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 277 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 117 optimal weight: 0.0570 chunk 23 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3699 r_free = 0.3699 target = 0.069543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047884 restraints weight = 69812.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.049123 restraints weight = 36391.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049927 restraints weight = 23904.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.050468 restraints weight = 18131.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050681 restraints weight = 15041.277| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11764 Z= 0.154 Angle : 0.620 10.793 16050 Z= 0.297 Chirality : 0.042 0.165 1848 Planarity : 0.003 0.029 2026 Dihedral : 5.242 62.550 1658 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.77 % Allowed : 12.01 % Favored : 86.22 % 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: 1.40 (0.19), residues: 718 sheet: -0.65 (0.44), residues: 148 loop : -1.85 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 26 TYR 0.016 0.001 TYR B 340 PHE 0.009 0.001 PHE A 277 TRP 0.017 0.002 TRP B 557 HIS 0.003 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (11742) covalent geometry : angle 0.60526 / 0.29 (16004) SS BOND : bond 0.00321 / 0.20 ( 20) SS BOND : angle 0.79008 / 0.59 ( 40) hydrogen bonds : bond 0.03793 / 2.56 ( 596) hydrogen bonds : angle 4.31221 / 3.04 ( 1722) link_NAG-ASN : bond 0.01349 / 0.68 ( 2) link_NAG-ASN : angle 6.96510 / 3.49 ( 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 81 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: A 405 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: A 414 MET cc_start: 0.9008 (tmm) cc_final: 0.8740 (tmm) REVERT: B 277 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: B 290 MET cc_start: 0.8461 (mmp) cc_final: 0.8148 (mmm) REVERT: B 405 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: B 414 MET cc_start: 0.9068 (tmm) cc_final: 0.8391 (tmm) REVERT: B 429 MET cc_start: 0.8357 (ttm) cc_final: 0.7940 (tpp) outliers start: 20 outliers final: 13 residues processed: 78 average time/residue: 0.0790 time to fit residues: 10.2765 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 117 LEU 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 277 PHE 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 53 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 58 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3682 r_free = 0.3682 target = 0.069074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047568 restraints weight = 71650.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048779 restraints weight = 37473.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049609 restraints weight = 24359.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050133 restraints weight = 18395.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050454 restraints weight = 15302.173| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11764 Z= 0.249 Angle : 0.698 12.834 16050 Z= 0.334 Chirality : 0.043 0.185 1848 Planarity : 0.003 0.028 2026 Dihedral : 5.331 61.753 1658 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.59 % Allowed : 12.28 % Favored : 86.13 % 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: -0.33 (0.21), residues: 1522 helix: 1.25 (0.19), residues: 718 sheet: -0.67 (0.43), residues: 148 loop : -1.83 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.021 0.001 TYR B 340 PHE 0.011 0.001 PHE A 277 TRP 0.015 0.002 TRP A 557 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (11742) covalent geometry : angle 0.68444 / 0.33 (16004) SS BOND : bond 0.00215 / 0.16 ( 20) SS BOND : angle 0.89941 / 0.67 ( 40) hydrogen bonds : bond 0.03983 / 2.70 ( 596) hydrogen bonds : angle 4.48696 / 3.17 ( 1722) link_NAG-ASN : bond 0.01149 / 0.58 ( 2) link_NAG-ASN : angle 6.97983 / 3.51 ( 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 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 405 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7920 (m-10) REVERT: A 414 MET cc_start: 0.8994 (tmm) cc_final: 0.8752 (tmm) REVERT: B 277 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: B 290 MET cc_start: 0.8499 (mmp) cc_final: 0.8153 (mmm) REVERT: B 405 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: B 414 MET cc_start: 0.9086 (tmm) cc_final: 0.8391 (tmm) REVERT: B 429 MET cc_start: 0.8467 (ttm) cc_final: 0.8011 (tpp) outliers start: 18 outliers final: 14 residues processed: 76 average time/residue: 0.0774 time to fit residues: 9.2724 Evaluate side-chains 77 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 117 LEU 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 277 PHE 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: 1.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3705 r_free = 0.3705 target = 0.069971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048462 restraints weight = 71129.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.049776 restraints weight = 36592.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050638 restraints weight = 23816.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051167 restraints weight = 17845.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051441 restraints weight = 14840.964| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11764 Z= 0.149 Angle : 0.635 13.037 16050 Z= 0.301 Chirality : 0.042 0.168 1848 Planarity : 0.003 0.029 2026 Dihedral : 5.253 61.655 1658 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.59 % Allowed : 12.01 % Favored : 86.40 % 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: -0.18 (0.22), residues: 1522 helix: 1.39 (0.19), residues: 718 sheet: -0.57 (0.43), residues: 148 loop : -1.80 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.016 0.001 TYR B 340 PHE 0.011 0.001 PHE B 277 TRP 0.015 0.002 TRP B 557 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11742) covalent geometry : angle 0.62053 / 0.30 (16004) SS BOND : bond 0.00182 / 0.13 ( 20) SS BOND : angle 0.81587 / 0.60 ( 40) hydrogen bonds : bond 0.03781 / 2.56 ( 596) hydrogen bonds : angle 4.33576 / 3.06 ( 1722) link_NAG-ASN : bond 0.01442 / 0.72 ( 2) link_NAG-ASN : angle 6.91688 / 3.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.31 seconds wall clock time: 33 minutes 47.84 seconds (2027.84 seconds total)