Starting phenix.real_space_refine on Sat Oct 24 06:42:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wqo_66178/10_2026/9wqo_66178.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wqo_66178/10_2026/9wqo_66178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wqo_66178/10_2026/9wqo_66178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wqo_66178/10_2026/9wqo_66178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wqo_66178/10_2026/9wqo_66178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wqo_66178/10_2026/9wqo_66178.map" } resolution = 2.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 95 5.16 5 Cl 2 4.86 5 C 7871 2.51 5 N 2029 2.21 5 O 2259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12256 Number of models: 1 Model: "" Number of chains: 4 Chain: "X" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6028 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 732} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 6094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6094 Classifications: {'peptide': 773} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 738} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {' CL': 1, 'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {' CL': 1, 'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 NAG X2002 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X2002 " occ=0.70 residue: pdb=" C1 NAG X2003 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X2003 " occ=0.70 residue: pdb=" C1 NAG X2004 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X2004 " occ=0.70 residue: pdb=" C1 NAG X2005 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X2005 " occ=0.70 residue: pdb=" C1 NAG Y2002 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2002 " occ=0.70 residue: pdb=" C1 NAG Y2003 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2003 " occ=0.70 residue: pdb=" C1 NAG Y2004 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2004 " occ=0.70 residue: pdb=" C1 NAG Y2005 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2005 " occ=0.70 Time building chain proxies: 2.95, per 1000 atoms: 0.24 Number of scatterers: 12256 At special positions: 0 Unit cell: (106.95, 92.07, 179.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 95 16.00 O 2259 8.00 N 2029 7.00 C 7871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS X 67 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 254 " - pdb=" SG CYS X 543 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 394 " distance=2.03 Simple disulfide: pdb=" SG CYS X 432 " - pdb=" SG CYS X 439 " distance=2.03 Simple disulfide: pdb=" SG CYS X 524 " - pdb=" SG CYS X 544 " distance=2.03 Simple disulfide: pdb=" SG CYS X 528 " - pdb=" SG CYS X 547 " distance=2.03 Simple disulfide: pdb=" SG CYS X 550 " - pdb=" SG CYS X 562 " distance=2.03 Simple disulfide: pdb=" SG CYS X 565 " - pdb=" SG CYS X 578 " distance=2.03 Simple disulfide: pdb=" SG CYS X 657 " - pdb=" SG CYS X 746 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 67 " - pdb=" SG CYS Y 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 254 " - pdb=" SG CYS Y 543 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 394 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 432 " - pdb=" SG CYS Y 439 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 524 " - pdb=" SG CYS Y 544 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 528 " - pdb=" SG CYS Y 547 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 550 " - pdb=" SG CYS Y 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 565 " - pdb=" SG CYS Y 578 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 657 " - pdb=" SG CYS Y 746 " distance=2.03 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 X2002 " - " ASN X 98 " " NAG X2003 " - " ASN X 223 " " NAG X2004 " - " ASN X 397 " " NAG X2005 " - " ASN X 515 " " NAG Y2002 " - " ASN Y 98 " " NAG Y2004 " - " ASN Y 397 " " NAG Y2005 " - " ASN Y 515 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 509.1 milliseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 51.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'X' and resid 58 through 62 removed outlier: 3.794A pdb=" N VAL X 62 " --> pdb=" O ALA X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 92 Processing helix chain 'X' and resid 111 through 124 Processing helix chain 'X' and resid 164 through 176 removed outlier: 3.675A pdb=" N LEU X 174 " --> pdb=" O GLN X 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 179 No H-bonds generated for 'chain 'X' and resid 177 through 179' Processing helix chain 'X' and resid 189 through 194 Processing helix chain 'X' and resid 207 through 222 removed outlier: 4.102A pdb=" N GLN X 211 " --> pdb=" O SER X 207 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR X 222 " --> pdb=" O ILE X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 252 Processing helix chain 'X' and resid 266 through 280 removed outlier: 3.939A pdb=" N ARG X 280 " --> pdb=" O LYS X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 292 through 306 Processing helix chain 'X' and resid 323 through 328 removed outlier: 4.135A pdb=" N ILE X 327 " --> pdb=" O ARG X 323 " (cutoff:3.500A) Processing helix chain 'X' and resid 330 through 335 Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 367 through 377 Processing helix chain 'X' and resid 409 through 432 Processing helix chain 'X' and resid 439 through 443 Processing helix chain 'X' and resid 446 through 456 Processing helix chain 'X' and resid 590 through 617 Processing helix chain 'X' and resid 620 through 626 Processing helix chain 'X' and resid 627 through 650 Proline residue: X 645 - end of helix removed outlier: 3.517A pdb=" N ALA X 650 " --> pdb=" O PHE X 646 " (cutoff:3.500A) Processing helix chain 'X' and resid 653 through 686 Processing helix chain 'X' and resid 703 through 728 removed outlier: 3.607A pdb=" N GLN X 717 " --> pdb=" O LEU X 713 " (cutoff:3.500A) Processing helix chain 'X' and resid 749 through 770 Proline residue: X 756 - end of helix removed outlier: 3.834A pdb=" N TYR X 770 " --> pdb=" O SER X 766 " (cutoff:3.500A) Processing helix chain 'X' and resid 772 through 777 removed outlier: 3.985A pdb=" N VAL X 777 " --> pdb=" O THR X 774 " (cutoff:3.500A) Processing helix chain 'X' and resid 786 through 807 removed outlier: 3.524A pdb=" N VAL X 802 " --> pdb=" O TRP X 798 " (cutoff:3.500A) Proline residue: X 803 - end of helix Processing helix chain 'X' and resid 810 through 841 Proline residue: X 833 - end of helix Processing helix chain 'Y' and resid 58 through 62 removed outlier: 3.732A pdb=" N VAL Y 62 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 92 Processing helix chain 'Y' and resid 111 through 124 Processing helix chain 'Y' and resid 164 through 176 Processing helix chain 'Y' and resid 177 through 179 No H-bonds generated for 'chain 'Y' and resid 177 through 179' Processing helix chain 'Y' and resid 189 through 194 Processing helix chain 'Y' and resid 207 through 222 removed outlier: 4.018A pdb=" N GLN Y 211 " --> pdb=" O SER Y 207 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR Y 222 " --> pdb=" O ILE Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 251 Processing helix chain 'Y' and resid 266 through 279 Processing helix chain 'Y' and resid 292 through 307 Processing helix chain 'Y' and resid 323 through 328 removed outlier: 4.146A pdb=" N ILE Y 327 " --> pdb=" O ARG Y 323 " (cutoff:3.500A) Processing helix chain 'Y' and resid 330 through 335 Processing helix chain 'Y' and resid 347 through 356 removed outlier: 3.702A pdb=" N LYS Y 356 " --> pdb=" O ASP Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 367 through 377 Processing helix chain 'Y' and resid 409 through 432 Processing helix chain 'Y' and resid 439 through 443 Processing helix chain 'Y' and resid 446 through 457 Processing helix chain 'Y' and resid 509 through 512 Processing helix chain 'Y' and resid 590 through 617 Processing helix chain 'Y' and resid 620 through 626 removed outlier: 3.562A pdb=" N SER Y 626 " --> pdb=" O VAL Y 622 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 649 Proline residue: Y 645 - end of helix Processing helix chain 'Y' and resid 653 through 686 removed outlier: 3.836A pdb=" N GLY Y 665 " --> pdb=" O ARG Y 661 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER Y 668 " --> pdb=" O VAL Y 664 " (cutoff:3.500A) Processing helix chain 'Y' and resid 702 through 728 Processing helix chain 'Y' and resid 749 through 770 Proline residue: Y 756 - end of helix Processing helix chain 'Y' and resid 782 through 807 Proline residue: Y 803 - end of helix removed outlier: 3.771A pdb=" N PHE Y 806 " --> pdb=" O VAL Y 802 " (cutoff:3.500A) Processing helix chain 'Y' and resid 810 through 839 Proline residue: Y 833 - end of helix Processing helix chain 'Y' and resid 841 through 845 removed outlier: 3.566A pdb=" N ARG Y 844 " --> pdb=" O LYS Y 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 39 through 41 removed outlier: 6.378A pdb=" N VAL X 45 " --> pdb=" O GLY X 102 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU X 104 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE X 47 " --> pdb=" O GLU X 104 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ARG X 106 " --> pdb=" O ILE X 47 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA X 49 " --> pdb=" O ARG X 106 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE X 46 " --> pdb=" O ALA X 157 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL X 159 " --> pdb=" O ILE X 46 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY X 48 " --> pdb=" O VAL X 159 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE X 183 " --> pdb=" O ALA X 157 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL X 159 " --> pdb=" O ILE X 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 254 through 261 removed outlier: 7.328A pdb=" N VAL X 227 " --> pdb=" O ALA X 256 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER X 258 " --> pdb=" O VAL X 227 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA X 229 " --> pdb=" O SER X 258 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS X 260 " --> pdb=" O ALA X 229 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS X 231 " --> pdb=" O LYS X 260 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR X 226 " --> pdb=" O VAL X 286 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL X 288 " --> pdb=" O TYR X 226 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER X 228 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR X 479 " --> pdb=" O THR X 499 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR X 499 " --> pdb=" O TYR X 479 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE X 481 " --> pdb=" O VAL X 497 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG X 491 " --> pdb=" O THR X 487 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 458 through 460 Processing sheet with id=AA4, first strand: chain 'X' and resid 532 through 535 Processing sheet with id=AA5, first strand: chain 'X' and resid 554 through 555 Processing sheet with id=AA6, first strand: chain 'X' and resid 569 through 571 Processing sheet with id=AA7, first strand: chain 'X' and resid 732 through 738 removed outlier: 6.730A pdb=" N GLU X 741 " --> pdb=" O PRO X 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 39 through 41 removed outlier: 6.346A pdb=" N VAL Y 45 " --> pdb=" O GLY Y 102 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU Y 104 " --> pdb=" O VAL Y 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE Y 47 " --> pdb=" O GLU Y 104 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ARG Y 106 " --> pdb=" O ILE Y 47 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA Y 49 " --> pdb=" O ARG Y 106 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE Y 46 " --> pdb=" O ILE Y 156 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY Y 158 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE Y 183 " --> pdb=" O ALA Y 157 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL Y 159 " --> pdb=" O ILE Y 183 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN Y 182 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 254 through 261 removed outlier: 7.504A pdb=" N VAL Y 227 " --> pdb=" O ALA Y 256 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER Y 258 " --> pdb=" O VAL Y 227 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA Y 229 " --> pdb=" O SER Y 258 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS Y 260 " --> pdb=" O ALA Y 229 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS Y 231 " --> pdb=" O LYS Y 260 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR Y 226 " --> pdb=" O VAL Y 286 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL Y 288 " --> pdb=" O TYR Y 226 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER Y 228 " --> pdb=" O VAL Y 288 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU Y 314 " --> pdb=" O ILE Y 338 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE Y 340 " --> pdb=" O LEU Y 314 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY Y 316 " --> pdb=" O ILE Y 340 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N LEU Y 342 " --> pdb=" O GLY Y 316 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR Y 479 " --> pdb=" O THR Y 499 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR Y 499 " --> pdb=" O TYR Y 479 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE Y 481 " --> pdb=" O VAL Y 497 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 458 through 460 Processing sheet with id=AB2, first strand: chain 'Y' and resid 532 through 535 Processing sheet with id=AB3, first strand: chain 'Y' and resid 554 through 558 removed outlier: 6.474A pdb=" N THR Y 561 " --> pdb=" O GLN Y 557 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 570 through 571 Processing sheet with id=AB5, first strand: chain 'Y' and resid 732 through 738 removed outlier: 7.018A pdb=" N GLU Y 741 " --> pdb=" O PRO Y 737 " (cutoff:3.500A) 632 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3890 1.34 - 1.46: 2963 1.46 - 1.58: 5538 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 12525 Sorted by residual: bond pdb=" C1 NAG X2004 " pdb=" O5 NAG X2004 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C GGL X2001 " pdb=" O GGL X2001 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG Y2004 " pdb=" O5 NAG Y2004 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C GGL Y2001 " pdb=" OXT GGL Y2001 " ideal model delta sigma weight residual 1.231 1.257 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C GGL X2001 " pdb=" OXT GGL X2001 " ideal model delta sigma weight residual 1.231 1.257 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 12520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 16617 1.27 - 2.54: 279 2.54 - 3.82: 74 3.82 - 5.09: 16 5.09 - 6.36: 7 Bond angle restraints: 16993 Sorted by residual: angle pdb=" CA CYS X 829 " pdb=" C CYS X 829 " pdb=" N MET X 830 " ideal model delta sigma weight residual 118.59 123.96 -5.37 1.63e+00 3.76e-01 1.09e+01 angle pdb=" OE1 GGL Y2001 " pdb=" CD GGL Y2001 " pdb=" OE2 GGL Y2001 " ideal model delta sigma weight residual 126.26 119.90 6.36 3.00e+00 1.11e-01 4.49e+00 angle pdb=" OE1 GGL X2001 " pdb=" CD GGL X2001 " pdb=" OE2 GGL X2001 " ideal model delta sigma weight residual 126.26 119.91 6.35 3.00e+00 1.11e-01 4.48e+00 angle pdb=" N TYR X 786 " pdb=" CA TYR X 786 " pdb=" C TYR X 786 " ideal model delta sigma weight residual 113.18 110.50 2.68 1.33e+00 5.65e-01 4.06e+00 angle pdb=" C VAL X 497 " pdb=" N GLY X 498 " pdb=" CA GLY X 498 " ideal model delta sigma weight residual 120.84 117.14 3.70 1.91e+00 2.74e-01 3.74e+00 ... (remaining 16988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6846 16.96 - 33.93: 661 33.93 - 50.89: 104 50.89 - 67.85: 25 67.85 - 84.82: 9 Dihedral angle restraints: 7645 sinusoidal: 3157 harmonic: 4488 Sorted by residual: dihedral pdb=" CA CYS X 528 " pdb=" CB CYS X 528 " pdb=" SG CYS X 528 " pdb=" SG CYS X 547 " ideal model delta sinusoidal sigma weight residual -73.00 -10.79 -62.21 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" CB CYS Y 550 " pdb=" SG CYS Y 550 " pdb=" SG CYS Y 562 " pdb=" CB CYS Y 562 " ideal model delta sinusoidal sigma weight residual -86.00 -56.12 -29.88 1 1.00e+01 1.00e-02 1.28e+01 dihedral pdb=" CA CYS Y 528 " pdb=" CB CYS Y 528 " pdb=" SG CYS Y 528 " pdb=" SG CYS Y 547 " ideal model delta sinusoidal sigma weight residual -73.00 -13.11 -59.89 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 7642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1259 0.032 - 0.063: 470 0.063 - 0.095: 136 0.095 - 0.127: 82 0.127 - 0.158: 6 Chirality restraints: 1953 Sorted by residual: chirality pdb=" C1 NAG X2005 " pdb=" ND2 ASN X 515 " pdb=" C2 NAG X2005 " pdb=" O5 NAG X2005 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA VAL Y 583 " pdb=" N VAL Y 583 " pdb=" C VAL Y 583 " pdb=" CB VAL Y 583 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE Y 340 " pdb=" N ILE Y 340 " pdb=" C ILE Y 340 " pdb=" CB ILE Y 340 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1950 not shown) Planarity restraints: 2138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR X 792 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C TYR X 792 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR X 792 " -0.011 2.00e-02 2.50e+03 pdb=" N THR X 793 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS X 795 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C CYS X 795 " 0.028 2.00e-02 2.50e+03 pdb=" O CYS X 795 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE X 796 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 794 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C THR X 794 " -0.028 2.00e-02 2.50e+03 pdb=" O THR X 794 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS X 795 " 0.009 2.00e-02 2.50e+03 ... (remaining 2135 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 150 2.65 - 3.21: 11296 3.21 - 3.78: 19492 3.78 - 4.34: 27041 4.34 - 4.90: 43965 Nonbonded interactions: 101944 Sorted by model distance: nonbonded pdb=" ND2 ASN Y 223 " pdb=" C1 NAG Y2003 " model vdw 2.091 3.550 nonbonded pdb=" O TYR Y 226 " pdb=" OG SER Y 522 " model vdw 2.177 3.040 nonbonded pdb=" O TYR X 226 " pdb=" OG SER X 522 " model vdw 2.206 3.040 nonbonded pdb=" O TYR X 810 " pdb=" OG1 THR X 814 " model vdw 2.212 3.040 nonbonded pdb=" O GLY X 828 " pdb=" OG1 THR X 832 " model vdw 2.216 3.040 ... (remaining 101939 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'X' and (resid 34 through 776 or resid 781 through 784 or (resid 785 and \ (name N or name CA or name C or name O or name CB )) or resid 786 through 2006)) \ selection = (chain 'Y' and (resid 34 through 683 or (resid 684 through 686 and (name N or na \ me CA or name C or name O or name CB )) or resid 702 through 842 or resid 2001 t \ hrough 2006)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.140 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12550 Z= 0.131 Angle : 0.471 6.359 17050 Z= 0.244 Chirality : 0.041 0.158 1953 Planarity : 0.003 0.032 2131 Dihedral : 13.356 84.818 4703 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.23 (0.22), residues: 1524 helix: 1.95 (0.19), residues: 732 sheet: -0.37 (0.39), residues: 168 loop : -0.13 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 537 TYR 0.010 0.001 TYR Y 792 PHE 0.011 0.001 PHE Y 290 TRP 0.007 0.001 TRP Y 367 HIS 0.002 0.000 HIS X 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12525) covalent geometry : angle 0.46993 / 0.24 (16993) SS BOND : bond 0.00177 / 0.10 ( 18) SS BOND : angle 0.65248 / 0.43 ( 36) hydrogen bonds : bond 0.11678 / 8.05 ( 632) hydrogen bonds : angle 5.30811 / 3.79 ( 1821) link_NAG-ASN : bond 0.00072 / 0.04 ( 7) link_NAG-ASN : angle 0.87157 / 0.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 747 ASN cc_start: 0.7160 (t0) cc_final: 0.5932 (t0) REVERT: Y 569 TRP cc_start: 0.6977 (m100) cc_final: 0.6588 (m100) REVERT: Y 646 PHE cc_start: 0.7432 (m-80) cc_final: 0.6934 (t80) REVERT: Y 648 LEU cc_start: 0.8918 (mt) cc_final: 0.8647 (mp) REVERT: Y 701 MET cc_start: 0.5798 (mmt) cc_final: 0.4826 (mmm) REVERT: Y 734 LEU cc_start: 0.8964 (mt) cc_final: 0.8751 (mt) REVERT: Y 773 LYS cc_start: 0.7990 (mttt) cc_final: 0.7680 (mmtt) REVERT: Y 791 MET cc_start: 0.7807 (mmp) cc_final: 0.7164 (mmm) REVERT: Y 825 VAL cc_start: 0.8378 (t) cc_final: 0.8175 (p) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 0.5903 time to fit residues: 154.5429 Evaluate side-chains 147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 384 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.0270 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 170 GLN X 235 ASN X 250 GLN X 406 GLN X 706 GLN ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Y 235 ASN Y 406 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090979 restraints weight = 26463.082| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.60 r_work: 0.3293 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12550 Z= 0.126 Angle : 0.547 11.922 17050 Z= 0.280 Chirality : 0.042 0.211 1953 Planarity : 0.004 0.036 2131 Dihedral : 6.450 54.675 1859 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.94 % Allowed : 10.01 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.26 (0.22), residues: 1524 helix: 2.10 (0.19), residues: 719 sheet: -0.64 (0.39), residues: 172 loop : -0.16 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 661 TYR 0.017 0.001 TYR X 792 PHE 0.011 0.001 PHE Y 350 TRP 0.009 0.001 TRP X 569 HIS 0.006 0.000 HIS X 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12525) covalent geometry : angle 0.54476 / 0.28 (16993) SS BOND : bond 0.00214 / 0.13 ( 18) SS BOND : angle 1.09673 / 0.95 ( 36) hydrogen bonds : bond 0.04275 / 2.95 ( 632) hydrogen bonds : angle 4.49968 / 3.22 ( 1821) link_NAG-ASN : bond 0.00104 / 0.06 ( 7) link_NAG-ASN : angle 0.88716 / 0.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 513 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: X 717 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: X 791 MET cc_start: 0.5246 (mmt) cc_final: 0.4668 (tmm) REVERT: Y 235 ASN cc_start: 0.8664 (t0) cc_final: 0.8434 (t0) REVERT: Y 546 ILE cc_start: 0.9034 (mt) cc_final: 0.8823 (mm) REVERT: Y 640 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7899 (mm) REVERT: Y 646 PHE cc_start: 0.7709 (m-80) cc_final: 0.7087 (t80) REVERT: Y 648 LEU cc_start: 0.9068 (mt) cc_final: 0.8852 (mp) REVERT: Y 701 MET cc_start: 0.5610 (mmt) cc_final: 0.4977 (mmm) REVERT: Y 825 VAL cc_start: 0.8629 (t) cc_final: 0.8409 (p) REVERT: Y 830 MET cc_start: 0.3616 (OUTLIER) cc_final: 0.3236 (mmm) outliers start: 26 outliers final: 10 residues processed: 162 average time/residue: 0.5783 time to fit residues: 102.0196 Evaluate side-chains 141 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 513 GLN Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 604 ILE Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 717 GLN Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain X residue 766 SER Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 706 GLN Chi-restraints excluded: chain Y residue 714 ILE Chi-restraints excluded: chain Y residue 822 SER Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [83, 48, 93, 29, 80, 32, 81, 57, 150, 12, 134] chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 235 ASN X 250 GLN ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.106913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088769 restraints weight = 26529.678| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.63 r_work: 0.3267 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12550 Z= 0.161 Angle : 0.557 11.366 17050 Z= 0.284 Chirality : 0.043 0.196 1953 Planarity : 0.004 0.031 2131 Dihedral : 6.100 52.156 1857 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.47 % Allowed : 11.73 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.21 (0.22), residues: 1524 helix: 2.01 (0.19), residues: 721 sheet: -0.61 (0.39), residues: 172 loop : -0.14 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 358 TYR 0.015 0.001 TYR X 786 PHE 0.016 0.001 PHE X 646 TRP 0.035 0.001 TRP Y 569 HIS 0.002 0.001 HIS X 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12525) covalent geometry : angle 0.55649 / 0.28 (16993) SS BOND : bond 0.00225 / 0.13 ( 18) SS BOND : angle 0.66778 / 0.50 ( 36) hydrogen bonds : bond 0.04295 / 2.96 ( 632) hydrogen bonds : angle 4.46194 / 3.20 ( 1821) link_NAG-ASN : bond 0.00102 / 0.07 ( 7) link_NAG-ASN : angle 0.98258 / 0.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 513 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: X 786 TYR cc_start: 0.6028 (m-10) cc_final: 0.5677 (m-10) REVERT: X 791 MET cc_start: 0.5257 (mmt) cc_final: 0.4627 (tmm) REVERT: Y 235 ASN cc_start: 0.8666 (t0) cc_final: 0.8400 (t0) REVERT: Y 640 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7931 (mm) REVERT: Y 646 PHE cc_start: 0.7732 (m-80) cc_final: 0.7086 (t80) REVERT: Y 648 LEU cc_start: 0.9066 (mt) cc_final: 0.8774 (mp) REVERT: Y 701 MET cc_start: 0.5600 (mmt) cc_final: 0.4943 (mmm) REVERT: Y 813 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8037 (tp) REVERT: Y 825 VAL cc_start: 0.8652 (t) cc_final: 0.8430 (p) REVERT: Y 830 MET cc_start: 0.3646 (OUTLIER) cc_final: 0.3185 (mmm) outliers start: 33 outliers final: 14 residues processed: 151 average time/residue: 0.5439 time to fit residues: 89.6064 Evaluate side-chains 141 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 513 GLN Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 604 ILE Chi-restraints excluded: chain X residue 620 THR Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 734 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 677 THR Chi-restraints excluded: chain Y residue 714 ILE Chi-restraints excluded: chain Y residue 813 ILE Chi-restraints excluded: chain Y residue 822 SER Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [70, 150, 54, 92, 140, 147, 75, 110, 50, 77, 6] chunk 70 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 6 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 235 ASN ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 706 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 = 0.3693 r_free = 0.3693 target = 0.105115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087213 restraints weight = 26342.261| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.59 r_work: 0.3236 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12550 Z= 0.228 Angle : 0.590 12.514 17050 Z= 0.301 Chirality : 0.044 0.194 1953 Planarity : 0.004 0.029 2131 Dihedral : 6.012 51.944 1857 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 2.62 % Allowed : 13.83 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.00 (0.22), residues: 1524 helix: 1.78 (0.19), residues: 721 sheet: -0.68 (0.40), residues: 157 loop : -0.20 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 478 TYR 0.025 0.001 TYR Y 792 PHE 0.017 0.002 PHE Y 290 TRP 0.015 0.001 TRP Y 569 HIS 0.003 0.001 HIS X 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (12525) covalent geometry : angle 0.58936 / 0.30 (16993) SS BOND : bond 0.00280 / 0.15 ( 18) SS BOND : angle 0.63548 / 0.46 ( 36) hydrogen bonds : bond 0.04651 / 3.21 ( 632) hydrogen bonds : angle 4.56974 / 3.27 ( 1821) link_NAG-ASN : bond 0.00216 / 0.13 ( 7) link_NAG-ASN : angle 1.10665 / 0.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 472 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8717 (mtmm) REVERT: X 727 MET cc_start: 0.6841 (mmm) cc_final: 0.6545 (tmm) REVERT: X 786 TYR cc_start: 0.6171 (m-10) cc_final: 0.5948 (m-10) REVERT: Y 235 ASN cc_start: 0.8713 (t0) cc_final: 0.8481 (t0) REVERT: Y 306 LEU cc_start: 0.9394 (tt) cc_final: 0.9162 (tm) REVERT: Y 640 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8080 (mm) REVERT: Y 646 PHE cc_start: 0.7771 (m-80) cc_final: 0.7180 (t80) REVERT: Y 701 MET cc_start: 0.5333 (mmt) cc_final: 0.4829 (mmm) REVERT: Y 825 VAL cc_start: 0.8691 (t) cc_final: 0.8476 (p) REVERT: Y 830 MET cc_start: 0.3796 (OUTLIER) cc_final: 0.3263 (mmm) outliers start: 35 outliers final: 17 residues processed: 145 average time/residue: 0.5183 time to fit residues: 82.6668 Evaluate side-chains 141 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 478 ARG Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 604 ILE Chi-restraints excluded: chain X residue 620 THR Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 722 VAL Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 714 ILE Chi-restraints excluded: chain Y residue 768 THR Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 822 SER Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [148, 0, 93, 144, 121, 125, 39, 149, 99, 116, 97] chunk 148 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 149 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 235 ASN ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 706 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 = 0.3714 r_free = 0.3714 target = 0.106555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088614 restraints weight = 26604.511| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.62 r_work: 0.3261 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12550 Z= 0.142 Angle : 0.557 9.894 17050 Z= 0.282 Chirality : 0.043 0.185 1953 Planarity : 0.003 0.041 2131 Dihedral : 5.816 51.657 1857 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 2.17 % Allowed : 14.65 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.06 (0.22), residues: 1524 helix: 1.88 (0.19), residues: 718 sheet: -0.96 (0.41), residues: 147 loop : -0.14 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 478 TYR 0.015 0.001 TYR Y 585 PHE 0.010 0.001 PHE X 350 TRP 0.017 0.001 TRP X 569 HIS 0.003 0.001 HIS X 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12525) covalent geometry : angle 0.55624 / 0.28 (16993) SS BOND : bond 0.00169 / 0.09 ( 18) SS BOND : angle 0.60785 / 0.46 ( 36) hydrogen bonds : bond 0.04189 / 2.86 ( 632) hydrogen bonds : angle 4.44200 / 3.17 ( 1821) link_NAG-ASN : bond 0.00089 / 0.06 ( 7) link_NAG-ASN : angle 1.01012 / 0.62 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 251 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: X 472 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8710 (mtmm) REVERT: Y 235 ASN cc_start: 0.8694 (t0) cc_final: 0.8437 (t0) REVERT: Y 640 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8012 (mm) REVERT: Y 646 PHE cc_start: 0.7713 (m-80) cc_final: 0.7061 (t80) REVERT: Y 701 MET cc_start: 0.5297 (mmt) cc_final: 0.4834 (mmm) REVERT: Y 747 ASN cc_start: 0.8092 (t0) cc_final: 0.7432 (p0) REVERT: Y 825 VAL cc_start: 0.8675 (t) cc_final: 0.8455 (p) REVERT: Y 830 MET cc_start: 0.3581 (OUTLIER) cc_final: 0.3075 (mmm) outliers start: 29 outliers final: 12 residues processed: 145 average time/residue: 0.5413 time to fit residues: 86.0362 Evaluate side-chains 135 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 251 GLU Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 663 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 768 THR Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [9, 38, 116, 7, 135, 122, 101, 128, 106, 60, 148] chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0010 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 148 optimal weight: 0.0370 overall best weight: 0.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 250 GLN X 501 HIS ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 706 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 = 0.3720 r_free = 0.3720 target = 0.106795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088865 restraints weight = 26389.764| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.61 r_work: 0.3280 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12550 Z= 0.138 Angle : 0.579 9.894 17050 Z= 0.291 Chirality : 0.043 0.196 1953 Planarity : 0.003 0.054 2131 Dihedral : 5.738 52.030 1857 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 2.24 % Allowed : 16.07 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.11 (0.22), residues: 1524 helix: 1.92 (0.19), residues: 718 sheet: -0.92 (0.40), residues: 152 loop : -0.12 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 478 TYR 0.013 0.001 TYR Y 585 PHE 0.018 0.001 PHE X 646 TRP 0.020 0.001 TRP X 569 HIS 0.002 0.000 HIS X 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12525) covalent geometry : angle 0.57813 / 0.29 (16993) SS BOND : bond 0.00175 / 0.10 ( 18) SS BOND : angle 0.62764 / 0.50 ( 36) hydrogen bonds : bond 0.04117 / 2.81 ( 632) hydrogen bonds : angle 4.36988 / 3.12 ( 1821) link_NAG-ASN : bond 0.00083 / 0.06 ( 7) link_NAG-ASN : angle 0.98802 / 0.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 251 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: X 472 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: X 727 MET cc_start: 0.6823 (mmm) cc_final: 0.6562 (tmm) REVERT: X 781 PHE cc_start: 0.2155 (OUTLIER) cc_final: 0.1629 (m-10) REVERT: X 835 MET cc_start: 0.2889 (mmt) cc_final: 0.2496 (mmt) REVERT: Y 235 ASN cc_start: 0.8672 (t0) cc_final: 0.8436 (t0) REVERT: Y 532 GLN cc_start: 0.8584 (mt0) cc_final: 0.7832 (tt0) REVERT: Y 640 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8038 (mm) REVERT: Y 646 PHE cc_start: 0.7708 (m-80) cc_final: 0.7047 (t80) REVERT: Y 701 MET cc_start: 0.5267 (mmt) cc_final: 0.4791 (mmm) REVERT: Y 794 THR cc_start: 0.7806 (m) cc_final: 0.7512 (t) REVERT: Y 825 VAL cc_start: 0.8679 (t) cc_final: 0.8464 (p) REVERT: Y 830 MET cc_start: 0.3631 (OUTLIER) cc_final: 0.3075 (mmm) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 0.5331 time to fit residues: 84.6389 Evaluate side-chains 142 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 251 GLU Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 478 ARG Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 734 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain X residue 781 PHE Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 714 ILE Chi-restraints excluded: chain Y residue 768 THR Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [88, 35, 98, 18, 72, 150, 53, 102, 44, 127, 59] chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 250 GLN ** X 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 706 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 = 0.3712 r_free = 0.3712 target = 0.107224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089244 restraints weight = 26490.484| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.64 r_work: 0.3243 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12550 Z= 0.192 Angle : 0.607 9.621 17050 Z= 0.305 Chirality : 0.044 0.203 1953 Planarity : 0.004 0.069 2131 Dihedral : 5.799 52.311 1857 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 16.97 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.00 (0.22), residues: 1524 helix: 1.77 (0.19), residues: 721 sheet: -0.96 (0.42), residues: 142 loop : -0.12 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 478 TYR 0.013 0.001 TYR Y 585 PHE 0.017 0.001 PHE Y 772 TRP 0.019 0.001 TRP X 569 HIS 0.002 0.001 HIS X 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (12525) covalent geometry : angle 0.60637 / 0.30 (16993) SS BOND : bond 0.00237 / 0.13 ( 18) SS BOND : angle 0.60794 / 0.44 ( 36) hydrogen bonds : bond 0.04390 / 3.00 ( 632) hydrogen bonds : angle 4.47533 / 3.21 ( 1821) link_NAG-ASN : bond 0.00163 / 0.10 ( 7) link_NAG-ASN : angle 1.05764 / 0.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 251 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: X 472 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8671 (mtmm) REVERT: X 560 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8243 (t80) REVERT: X 643 VAL cc_start: 0.8181 (m) cc_final: 0.7821 (p) REVERT: X 651 LYS cc_start: 0.5460 (mmpt) cc_final: 0.5230 (mppt) REVERT: X 747 ASN cc_start: 0.7147 (t0) cc_final: 0.6071 (p0) REVERT: X 781 PHE cc_start: 0.1968 (OUTLIER) cc_final: 0.1528 (m-10) REVERT: X 786 TYR cc_start: 0.6357 (m-10) cc_final: 0.6081 (m-10) REVERT: Y 235 ASN cc_start: 0.8669 (t0) cc_final: 0.8434 (t0) REVERT: Y 640 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8100 (mm) REVERT: Y 646 PHE cc_start: 0.7758 (m-80) cc_final: 0.7091 (t80) REVERT: Y 701 MET cc_start: 0.5228 (mmt) cc_final: 0.4733 (mmm) REVERT: Y 747 ASN cc_start: 0.8149 (t0) cc_final: 0.7418 (p0) REVERT: Y 794 THR cc_start: 0.7947 (m) cc_final: 0.7629 (t) REVERT: Y 825 VAL cc_start: 0.8677 (t) cc_final: 0.8463 (p) REVERT: Y 830 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.3003 (mmm) outliers start: 29 outliers final: 14 residues processed: 146 average time/residue: 0.4878 time to fit residues: 78.3791 Evaluate side-chains 144 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 251 GLU Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 560 PHE Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 620 THR Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 734 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain X residue 781 PHE Chi-restraints excluded: chain X residue 815 THR Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 640 LEU Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [53, 2, 91, 121, 142, 10, 38, 83, 65, 85, 74] chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 250 GLN ** X 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 706 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 = 0.105681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087691 restraints weight = 26299.436| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.64 r_work: 0.3248 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12550 Z= 0.176 Angle : 0.613 11.155 17050 Z= 0.308 Chirality : 0.044 0.197 1953 Planarity : 0.004 0.070 2131 Dihedral : 5.791 52.057 1857 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 2.24 % Allowed : 17.56 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 1.00 (0.22), residues: 1524 helix: 1.72 (0.19), residues: 723 sheet: -0.88 (0.42), residues: 140 loop : -0.09 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 478 TYR 0.015 0.001 TYR Y 585 PHE 0.013 0.001 PHE X 350 TRP 0.024 0.001 TRP X 569 HIS 0.002 0.001 HIS X 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (12525) covalent geometry : angle 0.61264 / 0.31 (16993) SS BOND : bond 0.00213 / 0.12 ( 18) SS BOND : angle 0.60866 / 0.47 ( 36) hydrogen bonds : bond 0.04361 / 2.96 ( 632) hydrogen bonds : angle 4.47239 / 3.20 ( 1821) link_NAG-ASN : bond 0.00138 / 0.09 ( 7) link_NAG-ASN : angle 1.04592 / 0.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 251 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: X 472 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8655 (mtmm) REVERT: X 560 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8204 (t80) REVERT: X 643 VAL cc_start: 0.7990 (m) cc_final: 0.7721 (p) REVERT: X 651 LYS cc_start: 0.5465 (mmpt) cc_final: 0.5218 (mppt) REVERT: X 717 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: X 727 MET cc_start: 0.6856 (mmm) cc_final: 0.6606 (tmm) REVERT: X 747 ASN cc_start: 0.7176 (t0) cc_final: 0.6141 (p0) REVERT: X 781 PHE cc_start: 0.2196 (OUTLIER) cc_final: 0.1850 (m-10) REVERT: X 835 MET cc_start: 0.3089 (mmt) cc_final: 0.2844 (mmt) REVERT: Y 235 ASN cc_start: 0.8678 (t0) cc_final: 0.8435 (t0) REVERT: Y 646 PHE cc_start: 0.7768 (m-80) cc_final: 0.7088 (t80) REVERT: Y 701 MET cc_start: 0.5251 (mmt) cc_final: 0.4748 (mmm) REVERT: Y 747 ASN cc_start: 0.8134 (t0) cc_final: 0.7408 (p0) REVERT: Y 794 THR cc_start: 0.7934 (m) cc_final: 0.7582 (t) REVERT: Y 813 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8032 (tp) REVERT: Y 825 VAL cc_start: 0.8674 (t) cc_final: 0.8459 (p) REVERT: Y 830 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.2954 (mmm) outliers start: 30 outliers final: 16 residues processed: 143 average time/residue: 0.4817 time to fit residues: 75.9608 Evaluate side-chains 144 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 251 GLU Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 560 PHE Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 616 LEU Chi-restraints excluded: chain X residue 620 THR Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 717 GLN Chi-restraints excluded: chain X residue 734 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain X residue 781 PHE Chi-restraints excluded: chain X residue 815 THR Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 714 ILE Chi-restraints excluded: chain Y residue 813 ILE Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [22, 120, 40, 114, 42, 67, 0, 112, 97, 48, 98] chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 231 HIS X 250 GLN ** X 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 706 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 = 0.3672 r_free = 0.3672 target = 0.103848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086041 restraints weight = 26220.416| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.62 r_work: 0.3216 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12550 Z= 0.256 Angle : 0.671 11.263 17050 Z= 0.337 Chirality : 0.046 0.365 1953 Planarity : 0.004 0.067 2131 Dihedral : 5.962 52.354 1857 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.32 % Allowed : 17.71 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.77 (0.21), residues: 1524 helix: 1.45 (0.19), residues: 724 sheet: -0.94 (0.43), residues: 135 loop : -0.12 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 478 TYR 0.016 0.002 TYR Y 585 PHE 0.021 0.002 PHE Y 772 TRP 0.024 0.001 TRP X 569 HIS 0.003 0.001 HIS Y 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (12525) covalent geometry : angle 0.66997 / 0.34 (16993) SS BOND : bond 0.00310 / 0.17 ( 18) SS BOND : angle 0.68691 / 0.54 ( 36) hydrogen bonds : bond 0.04817 / 3.32 ( 632) hydrogen bonds : angle 4.65526 / 3.32 ( 1821) link_NAG-ASN : bond 0.00280 / 0.16 ( 7) link_NAG-ASN : angle 1.18260 / 0.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 472 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8638 (mtmm) REVERT: X 643 VAL cc_start: 0.8081 (m) cc_final: 0.7802 (p) REVERT: X 717 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: X 747 ASN cc_start: 0.7258 (t0) cc_final: 0.6168 (p0) REVERT: Y 681 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7293 (ttm-80) REVERT: Y 747 ASN cc_start: 0.8185 (t0) cc_final: 0.7426 (p0) REVERT: Y 794 THR cc_start: 0.7989 (m) cc_final: 0.7672 (t) REVERT: Y 813 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8113 (tp) REVERT: Y 825 VAL cc_start: 0.8736 (t) cc_final: 0.8510 (p) REVERT: Y 830 MET cc_start: 0.3839 (OUTLIER) cc_final: 0.3039 (mmm) outliers start: 31 outliers final: 17 residues processed: 152 average time/residue: 0.4979 time to fit residues: 83.1665 Evaluate side-chains 144 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 604 ILE Chi-restraints excluded: chain X residue 620 THR Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 717 GLN Chi-restraints excluded: chain X residue 734 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain X residue 815 THR Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 768 THR Chi-restraints excluded: chain Y residue 781 PHE Chi-restraints excluded: chain Y residue 813 ILE Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [67, 88, 51, 128, 19, 141, 73, 62, 42, 13, 15] chunk 67 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 chunk 19 optimal weight: 0.0980 chunk 141 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 250 GLN ** X 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN Y 250 GLN ** Y 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090005 restraints weight = 26469.347| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.66 r_work: 0.3255 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12550 Z= 0.142 Angle : 0.644 12.304 17050 Z= 0.319 Chirality : 0.044 0.361 1953 Planarity : 0.004 0.066 2131 Dihedral : 5.790 51.633 1857 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 1.79 % Allowed : 18.46 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.89 (0.22), residues: 1524 helix: 1.58 (0.19), residues: 725 sheet: -0.91 (0.42), residues: 140 loop : -0.10 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 348 TYR 0.025 0.001 TYR Y 736 PHE 0.012 0.001 PHE Y 772 TRP 0.035 0.001 TRP X 569 HIS 0.001 0.000 HIS X 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (12525) covalent geometry : angle 0.64335 / 0.32 (16993) SS BOND : bond 0.00162 / 0.09 ( 18) SS BOND : angle 0.62923 / 0.48 ( 36) hydrogen bonds : bond 0.04247 / 2.88 ( 632) hydrogen bonds : angle 4.47942 / 3.19 ( 1821) link_NAG-ASN : bond 0.00096 / 0.06 ( 7) link_NAG-ASN : angle 1.01010 / 0.60 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 251 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: X 472 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8661 (mtmm) REVERT: X 643 VAL cc_start: 0.7818 (m) cc_final: 0.7561 (p) REVERT: X 651 LYS cc_start: 0.5424 (mmpt) cc_final: 0.5091 (mppt) REVERT: X 709 ILE cc_start: 0.5840 (pp) cc_final: 0.5526 (pp) REVERT: X 747 ASN cc_start: 0.7255 (t0) cc_final: 0.6228 (p0) REVERT: X 835 MET cc_start: 0.2914 (mmt) cc_final: 0.2524 (mmt) REVERT: Y 681 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7458 (ttm110) REVERT: Y 747 ASN cc_start: 0.8124 (t0) cc_final: 0.7407 (p0) REVERT: Y 794 THR cc_start: 0.7928 (m) cc_final: 0.7633 (t) REVERT: Y 813 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (tp) REVERT: Y 825 VAL cc_start: 0.8710 (t) cc_final: 0.8499 (p) REVERT: Y 830 MET cc_start: 0.3654 (OUTLIER) cc_final: 0.3030 (mmm) outliers start: 24 outliers final: 16 residues processed: 138 average time/residue: 0.5127 time to fit residues: 77.6958 Evaluate side-chains 140 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 82 MET Chi-restraints excluded: chain X residue 251 GLU Chi-restraints excluded: chain X residue 472 LYS Chi-restraints excluded: chain X residue 535 VAL Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 620 THR Chi-restraints excluded: chain X residue 644 CYS Chi-restraints excluded: chain X residue 655 THR Chi-restraints excluded: chain X residue 734 LEU Chi-restraints excluded: chain X residue 748 THR Chi-restraints excluded: chain X residue 815 THR Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 253 LEU Chi-restraints excluded: chain Y residue 455 ILE Chi-restraints excluded: chain Y residue 647 THR Chi-restraints excluded: chain Y residue 714 ILE Chi-restraints excluded: chain Y residue 781 PHE Chi-restraints excluded: chain Y residue 813 ILE Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 830 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [3, 6, 16, 144, 77, 115, 72, 111, 14, 13, 23] chunk 3 optimal weight: 0.0370 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 250 GLN ** X 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN ** Y 706 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 = 0.3720 r_free = 0.3720 target = 0.106889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088791 restraints weight = 26203.002| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.65 r_work: 0.3268 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12550 Z= 0.135 Angle : 0.637 12.731 17050 Z= 0.314 Chirality : 0.044 0.353 1953 Planarity : 0.004 0.065 2131 Dihedral : 5.709 52.062 1857 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.49 % Allowed : 18.83 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.99 (0.22), residues: 1524 helix: 1.71 (0.19), residues: 722 sheet: -1.12 (0.41), residues: 150 loop : 0.00 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 348 TYR 0.013 0.001 TYR Y 585 PHE 0.016 0.001 PHE Y 772 TRP 0.042 0.001 TRP X 569 HIS 0.001 0.000 HIS X 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (12525) covalent geometry : angle 0.63628 / 0.31 (16993) SS BOND : bond 0.00152 / 0.09 ( 18) SS BOND : angle 0.62988 / 0.47 ( 36) hydrogen bonds : bond 0.04094 / 2.80 ( 632) hydrogen bonds : angle 4.39392 / 3.12 ( 1821) link_NAG-ASN : bond 0.00067 / 0.05 ( 7) link_NAG-ASN : angle 0.95362 / 0.58 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3533.29 seconds wall clock time: 61 minutes 9.38 seconds (3669.38 seconds total)