Starting phenix.real_space_refine on Fri Feb 16 08:47:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5d_29740/02_2024/8g5d_29740_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.170 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 P 18 5.49 5 S 102 5.16 5 C 9433 2.51 5 N 2507 2.21 5 O 2792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1009": "OE1" <-> "OE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 861": "OE1" <-> "OE2" Residue "B GLU 1009": "OE1" <-> "OE2" Residue "B GLU 1046": "OE1" <-> "OE2" Residue "B GLU 1047": "OE1" <-> "OE2" Residue "B GLU 1050": "OE1" <-> "OE2" Residue "C GLU 851": "OE1" <-> "OE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "C GLU 1011": "OE1" <-> "OE2" Residue "C GLU 1046": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 683": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D GLU 781": "OE1" <-> "OE2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D GLU 847": "OE1" <-> "OE2" Residue "D GLU 861": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14852 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 8012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1037, 8009 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 987} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1037, 8009 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 987} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8180 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 152 Unusual residues: {'ACO': 1, 'ADP': 1, 'OAA': 1, 'PO4': 1, 'Q5B': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 12.23, per 1000 atoms: 0.82 Number of scatterers: 14852 At special positions: 0 Unit cell: (131.97, 112.05, 133.63, 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) S 102 16.00 P 18 15.00 O 2792 8.00 N 2507 7.00 C 9433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 4.0 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 8 sheets defined 48.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 4.236A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1002 through 1015 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1045 through 1054 Processing helix chain 'A' and resid 1056 through 1079 removed outlier: 3.849A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 869 through 878 Processing helix chain 'B' and resid 884 through 896 Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 4.237A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1002 through 1015 Processing helix chain 'B' and resid 1025 through 1039 Processing helix chain 'B' and resid 1045 through 1054 Processing helix chain 'B' and resid 1056 through 1079 removed outlier: 3.834A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1090 No H-bonds generated for 'chain 'B' and resid 1088 through 1090' Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 878 Processing helix chain 'C' and resid 884 through 896 Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.192A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 952 Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1025 through 1039 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1056 through 1079 removed outlier: 3.941A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 165 through 168 No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 175 through 194 removed outlier: 5.278A pdb=" N GLU D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE D 180 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP D 194 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 removed outlier: 4.350A pdb=" N TYR D 227 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 313 through 327 Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 384 through 397 Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 575 through 587 removed outlier: 4.725A pdb=" N TYR D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 665 through 677 Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.629A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 772 through 782 Processing helix chain 'D' and resid 793 through 805 Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 878 Processing helix chain 'D' and resid 884 through 896 Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 4.206A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 952 Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1002 through 1017 Processing helix chain 'D' and resid 1025 through 1039 Processing helix chain 'D' and resid 1045 through 1054 Processing helix chain 'D' and resid 1056 through 1079 removed outlier: 3.848A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.643A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 31 through 34 removed outlier: 3.584A pdb=" N LEU D 76 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL D 57 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL D 74 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL D 72 " --> pdb=" O PRO D 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 93 through 95 Processing sheet with id= D, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'D' and resid 263 through 268 Processing sheet with id= F, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.130A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 619 through 621 removed outlier: 7.672A pdb=" N VAL D 501 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET D 529 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 14.136A pdb=" N ALA D 527 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU D 549 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N MET D 529 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 739 through 745 removed outlier: 7.552A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1830 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: 5.28 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2463 1.32 - 1.46: 4517 1.46 - 1.59: 7955 1.59 - 1.73: 33 1.73 - 1.86: 168 Bond restraints: 15136 Sorted by residual: bond pdb=" C5 Q5B D3303 " pdb=" O7 Q5B D3303 " ideal model delta sigma weight residual 1.313 1.577 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C5 Q5B D3303 " pdb=" C6 Q5B D3303 " ideal model delta sigma weight residual 1.563 1.317 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C7 Q5B D3303 " pdb=" C8 Q5B D3303 " ideal model delta sigma weight residual 1.349 1.508 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C5A ACO A3301 " pdb=" C6A ACO A3301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5A ACO C3301 " pdb=" C6A ACO C3301 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.14e+01 ... (remaining 15131 not shown) Histogram of bond angle deviations from ideal: 98.90 - 106.86: 537 106.86 - 114.81: 8963 114.81 - 122.77: 9802 122.77 - 130.73: 1123 130.73 - 138.68: 77 Bond angle restraints: 20502 Sorted by residual: angle pdb=" P1A ACO C3301 " pdb=" O3A ACO C3301 " pdb=" P2A ACO C3301 " ideal model delta sigma weight residual 136.83 124.29 12.54 1.00e+00 1.00e+00 1.57e+02 angle pdb=" P1A ACO D3301 " pdb=" O3A ACO D3301 " pdb=" P2A ACO D3301 " ideal model delta sigma weight residual 136.83 124.98 11.85 1.00e+00 1.00e+00 1.40e+02 angle pdb=" P1A ACO B3301 " pdb=" O3A ACO B3301 " pdb=" P2A ACO B3301 " ideal model delta sigma weight residual 136.83 125.32 11.51 1.00e+00 1.00e+00 1.33e+02 angle pdb=" P1A ACO A3301 " pdb=" O3A ACO A3301 " pdb=" P2A ACO A3301 " ideal model delta sigma weight residual 136.83 126.80 10.03 1.00e+00 1.00e+00 1.01e+02 angle pdb=" C5A ACO A3301 " pdb=" C4A ACO A3301 " pdb=" N3A ACO A3301 " ideal model delta sigma weight residual 126.80 118.57 8.23 1.00e+00 1.00e+00 6.77e+01 ... (remaining 20497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 8696 35.76 - 71.51: 351 71.51 - 107.27: 43 107.27 - 143.02: 2 143.02 - 178.78: 6 Dihedral angle restraints: 9098 sinusoidal: 3774 harmonic: 5324 Sorted by residual: dihedral pdb=" C5' ADP D3304 " pdb=" O5' ADP D3304 " pdb=" PA ADP D3304 " pdb=" O2A ADP D3304 " ideal model delta sinusoidal sigma weight residual 300.00 138.11 161.90 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D3304 " pdb=" O3A ADP D3304 " pdb=" PA ADP D3304 " pdb=" PB ADP D3304 " ideal model delta sinusoidal sigma weight residual -60.00 70.69 -130.69 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP D3304 " pdb=" O3A ADP D3304 " pdb=" PB ADP D3304 " pdb=" PA ADP D3304 " ideal model delta sinusoidal sigma weight residual -60.00 47.07 -107.07 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 9095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2127 0.094 - 0.188: 120 0.188 - 0.283: 5 0.283 - 0.377: 1 0.377 - 0.471: 1 Chirality restraints: 2254 Sorted by residual: chirality pdb=" C7 Q5B D3303 " pdb=" C6 Q5B D3303 " pdb=" C8 Q5B D3303 " pdb=" O8 Q5B D3303 " both_signs ideal model delta sigma weight residual False 2.37 2.84 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C14 Q5B D3303 " pdb=" C1 Q5B D3303 " pdb=" C15 Q5B D3303 " pdb=" O21 Q5B D3303 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA THR D1014 " pdb=" N THR D1014 " pdb=" C THR D1014 " pdb=" CB THR D1014 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2251 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO B3301 " -0.211 2.00e-02 2.50e+03 1.81e-01 4.07e+02 pdb=" C5P ACO B3301 " 0.050 2.00e-02 2.50e+03 pdb=" C6P ACO B3301 " 0.037 2.00e-02 2.50e+03 pdb=" N4P ACO B3301 " 0.293 2.00e-02 2.50e+03 pdb=" O5P ACO B3301 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO D3301 " 0.155 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C5P ACO D3301 " -0.045 2.00e-02 2.50e+03 pdb=" C6P ACO D3301 " 0.116 2.00e-02 2.50e+03 pdb=" N4P ACO D3301 " -0.199 2.00e-02 2.50e+03 pdb=" O5P ACO D3301 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C3301 " -0.138 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C9P ACO C3301 " 0.048 2.00e-02 2.50e+03 pdb=" CAP ACO C3301 " -0.106 2.00e-02 2.50e+03 pdb=" N8P ACO C3301 " 0.179 2.00e-02 2.50e+03 pdb=" O9P ACO C3301 " 0.017 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1679 2.75 - 3.28: 14900 3.28 - 3.82: 27166 3.82 - 4.36: 33855 4.36 - 4.90: 55043 Nonbonded interactions: 132643 Sorted by model distance: nonbonded pdb=" OE1 GLU A 847 " pdb=" NH2 ARG D1085 " model vdw 2.207 2.520 nonbonded pdb=" O LEU D 85 " pdb=" N LEU D 89 " model vdw 2.228 2.520 nonbonded pdb=" OG SER B 843 " pdb=" OD1 ASP D1075 " model vdw 2.242 2.440 nonbonded pdb=" O GLY D 664 " pdb=" OG SER D 667 " model vdw 2.242 2.440 nonbonded pdb=" O LYS D 265 " pdb=" OH TYR D 319 " model vdw 2.252 2.440 ... (remaining 132638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.40 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: 0.510 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: 3.290 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 50.560 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.008 0.264 15136 Z= 0.495 Angle : 0.894 16.160 20502 Z= 0.512 Chirality : 0.051 0.471 2254 Planarity : 0.008 0.181 2595 Dihedral : 19.291 178.781 5712 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.52 % Allowed : 21.61 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1865 helix: 1.12 (0.16), residues: 1004 sheet: 0.16 (0.44), residues: 143 loop : -0.33 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 827 HIS 0.007 0.002 HIS C1086 PHE 0.020 0.002 PHE D 189 TYR 0.017 0.003 TYR D 120 ARG 0.011 0.001 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 1.602 Fit side-chains REVERT: A 940 ASP cc_start: 0.7420 (t70) cc_final: 0.7186 (t70) REVERT: A 965 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6742 (mttt) REVERT: A 1089 ASP cc_start: 0.7386 (p0) cc_final: 0.7042 (p0) REVERT: A 1094 VAL cc_start: 0.8575 (t) cc_final: 0.8337 (m) REVERT: B 965 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7884 (ttmm) REVERT: B 1089 ASP cc_start: 0.7418 (p0) cc_final: 0.7001 (p0) REVERT: C 866 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6701 (mp0) REVERT: D 56 VAL cc_start: 0.7269 (p) cc_final: 0.7032 (p) REVERT: D 107 ILE cc_start: 0.8074 (mt) cc_final: 0.7873 (mm) REVERT: D 788 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7337 (ttt90) REVERT: D 820 THR cc_start: 0.8075 (m) cc_final: 0.7856 (t) REVERT: D 864 LYS cc_start: 0.7442 (mtpt) cc_final: 0.7005 (tttp) outliers start: 8 outliers final: 1 residues processed: 203 average time/residue: 1.5045 time to fit residues: 332.4035 Evaluate side-chains 187 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 0.0270 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 overall best weight: 2.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 961 ASN A1020 ASN A1058 ASN B 982 ASN C 961 ASN C1024 ASN D 27 ASN D 45 GLN ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 ASN D 757 GLN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15136 Z= 0.232 Angle : 0.556 8.481 20502 Z= 0.286 Chirality : 0.043 0.239 2254 Planarity : 0.004 0.071 2595 Dihedral : 14.352 175.542 2285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 18.47 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1865 helix: 1.13 (0.16), residues: 1004 sheet: 0.13 (0.44), residues: 143 loop : -0.33 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 40 HIS 0.005 0.001 HIS C1086 PHE 0.015 0.002 PHE D1061 TYR 0.012 0.002 TYR D 120 ARG 0.008 0.000 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 867 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7072 (ptm) REVERT: A 888 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6794 (mm-40) REVERT: A 940 ASP cc_start: 0.7334 (t70) cc_final: 0.7087 (t70) REVERT: A 996 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6196 (mt0) REVERT: A 1089 ASP cc_start: 0.7344 (p0) cc_final: 0.7000 (p0) REVERT: B 948 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7463 (tttt) REVERT: B 1089 ASP cc_start: 0.7331 (p0) cc_final: 0.6925 (p0) REVERT: C 971 MET cc_start: 0.7717 (mmp) cc_final: 0.7503 (mmm) REVERT: D 28 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6976 (mtp180) REVERT: D 103 LYS cc_start: 0.7462 (mtmm) cc_final: 0.6784 (pttm) REVERT: D 107 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7594 (mm) REVERT: D 121 VAL cc_start: 0.7997 (t) cc_final: 0.7598 (p) REVERT: D 230 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7527 (ttpt) REVERT: D 327 MET cc_start: 0.7809 (ttm) cc_final: 0.7478 (mtm) REVERT: D 732 LYS cc_start: 0.8086 (tppp) cc_final: 0.7817 (tppp) REVERT: D 820 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7880 (t) REVERT: D 864 LYS cc_start: 0.7582 (mtpt) cc_final: 0.7150 (tttp) outliers start: 44 outliers final: 12 residues processed: 220 average time/residue: 1.6050 time to fit residues: 383.0718 Evaluate side-chains 200 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN A1058 ASN D 332 HIS D 757 GLN D 982 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15136 Z= 0.285 Angle : 0.578 7.646 20502 Z= 0.297 Chirality : 0.045 0.243 2254 Planarity : 0.004 0.059 2595 Dihedral : 13.453 170.275 2278 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.20 % Allowed : 17.62 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1865 helix: 1.10 (0.16), residues: 990 sheet: 0.11 (0.44), residues: 144 loop : -0.31 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 40 HIS 0.005 0.001 HIS C1086 PHE 0.015 0.002 PHE D1061 TYR 0.013 0.002 TYR D 304 ARG 0.009 0.001 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 888 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6782 (mm-40) REVERT: A 940 ASP cc_start: 0.7462 (t70) cc_final: 0.7243 (t70) REVERT: A 976 ARG cc_start: 0.6727 (ptt-90) cc_final: 0.6152 (ptp90) REVERT: A 996 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6164 (mt0) REVERT: A 1049 ASP cc_start: 0.8120 (m-30) cc_final: 0.7787 (m-30) REVERT: A 1089 ASP cc_start: 0.7358 (p0) cc_final: 0.7075 (p0) REVERT: B 851 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 864 LYS cc_start: 0.7517 (mttp) cc_final: 0.7172 (ttmm) REVERT: B 888 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6084 (mp10) REVERT: B 891 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7252 (mt-10) REVERT: B 948 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7448 (tttt) REVERT: B 965 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7956 (ttmm) REVERT: B 1089 ASP cc_start: 0.7388 (p0) cc_final: 0.6949 (p0) REVERT: C 892 MET cc_start: 0.7631 (mtp) cc_final: 0.7418 (mtp) REVERT: C 995 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6580 (mpt-90) REVERT: C 996 GLN cc_start: 0.7359 (mt0) cc_final: 0.7106 (mt0) REVERT: D 103 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6752 (pttm) REVERT: D 107 ILE cc_start: 0.7941 (mt) cc_final: 0.7572 (mm) REVERT: D 121 VAL cc_start: 0.8047 (t) cc_final: 0.7640 (p) REVERT: D 230 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7547 (ttpt) REVERT: D 313 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6419 (tm-30) REVERT: D 732 LYS cc_start: 0.8057 (tppp) cc_final: 0.7777 (tppp) REVERT: D 820 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7911 (t) REVERT: D 835 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5970 (mtm110) REVERT: D 848 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.5742 (ptt-90) REVERT: D 864 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7078 (tttp) REVERT: D 978 LYS cc_start: 0.6250 (mtmm) cc_final: 0.5764 (mttt) outliers start: 49 outliers final: 18 residues processed: 220 average time/residue: 1.6291 time to fit residues: 388.3825 Evaluate side-chains 208 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 851 GLU Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 864 LYS Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 0.0170 chunk 18 optimal weight: 0.0030 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN A1058 ASN A1081 GLN B 850 GLN ** C 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN C1020 ASN D 757 GLN ** D1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15136 Z= 0.149 Angle : 0.494 7.863 20502 Z= 0.250 Chirality : 0.041 0.213 2254 Planarity : 0.004 0.052 2595 Dihedral : 12.624 166.887 2278 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.09 % Allowed : 19.32 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1865 helix: 1.30 (0.16), residues: 999 sheet: 0.06 (0.44), residues: 149 loop : -0.17 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 40 HIS 0.002 0.001 HIS C1086 PHE 0.011 0.001 PHE B1061 TYR 0.014 0.001 TYR D 213 ARG 0.008 0.000 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.619 Fit side-chains REVERT: A 881 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6778 (tmt170) REVERT: A 940 ASP cc_start: 0.7292 (t70) cc_final: 0.7057 (t70) REVERT: A 965 LYS cc_start: 0.7768 (ptpp) cc_final: 0.6912 (mttt) REVERT: A 976 ARG cc_start: 0.6671 (ptt-90) cc_final: 0.6144 (ptp90) REVERT: A 996 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6088 (mt0) REVERT: B 864 LYS cc_start: 0.7487 (mttp) cc_final: 0.7148 (tttp) REVERT: B 888 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: B 948 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7510 (tttt) REVERT: B 965 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7874 (ttmm) REVERT: B 1089 ASP cc_start: 0.7369 (p0) cc_final: 0.6983 (p0) REVERT: C 892 MET cc_start: 0.7599 (mtp) cc_final: 0.7384 (mtp) REVERT: C 996 GLN cc_start: 0.7292 (mt0) cc_final: 0.7061 (mt0) REVERT: D 103 LYS cc_start: 0.7376 (mtmm) cc_final: 0.6706 (pttm) REVERT: D 107 ILE cc_start: 0.7918 (mt) cc_final: 0.7517 (mm) REVERT: D 121 VAL cc_start: 0.8019 (t) cc_final: 0.7660 (p) REVERT: D 230 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7531 (ttpt) REVERT: D 308 SER cc_start: 0.7741 (OUTLIER) cc_final: 0.7468 (p) REVERT: D 313 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: D 327 MET cc_start: 0.7708 (ttm) cc_final: 0.7478 (mtm) REVERT: D 820 THR cc_start: 0.8080 (m) cc_final: 0.7845 (t) REVERT: D 835 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5908 (mtm110) REVERT: D 864 LYS cc_start: 0.7427 (mtpt) cc_final: 0.7085 (tmtm) outliers start: 32 outliers final: 10 residues processed: 209 average time/residue: 1.5454 time to fit residues: 350.7765 Evaluate side-chains 200 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN A1058 ASN C 975 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS D 757 GLN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.108 15136 Z= 0.651 Angle : 0.788 9.361 20502 Z= 0.406 Chirality : 0.058 0.330 2254 Planarity : 0.006 0.052 2595 Dihedral : 13.346 164.686 2278 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.27 % Favored : 96.51 % Rotamer: Outliers : 3.72 % Allowed : 17.95 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1865 helix: 0.73 (0.16), residues: 980 sheet: 0.26 (0.44), residues: 139 loop : -0.44 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 827 HIS 0.010 0.002 HIS C 997 PHE 0.025 0.003 PHE D 242 TYR 0.033 0.004 TYR D 213 ARG 0.011 0.001 ARG A1085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 185 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 835 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5526 (mpp-170) REVERT: A 888 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6894 (mm-40) REVERT: A 996 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6731 (mp10) REVERT: A 1009 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 864 LYS cc_start: 0.7356 (mttp) cc_final: 0.7030 (tttp) REVERT: B 948 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7515 (tttt) REVERT: B 965 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7972 (ttmm) REVERT: B 1089 ASP cc_start: 0.7368 (p0) cc_final: 0.6934 (p0) REVERT: C 861 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6705 (tt0) REVERT: C 866 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: C 995 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6572 (mpt-90) REVERT: C 996 GLN cc_start: 0.7427 (mt0) cc_final: 0.7158 (mt0) REVERT: C 1050 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: D 103 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6881 (pttm) REVERT: D 107 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7653 (mm) REVERT: D 121 VAL cc_start: 0.8083 (t) cc_final: 0.7605 (p) REVERT: D 210 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6060 (t0) REVERT: D 230 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7634 (ttmt) REVERT: D 504 MET cc_start: 0.7939 (tpp) cc_final: 0.7514 (tpp) REVERT: D 820 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8041 (t) REVERT: D 835 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5654 (mmp80) REVERT: D 848 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.5787 (ptt-90) REVERT: D 864 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7022 (tmtm) REVERT: D 978 LYS cc_start: 0.6514 (mtmm) cc_final: 0.5880 (mmmt) outliers start: 57 outliers final: 24 residues processed: 225 average time/residue: 1.6326 time to fit residues: 398.1536 Evaluate side-chains 214 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 861 GLU Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 754 SER Chi-restraints excluded: chain D residue 799 SER Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 864 LYS Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 850 GLN C 975 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS D 615 GLN D 757 GLN D 982 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15136 Z= 0.214 Angle : 0.556 9.694 20502 Z= 0.284 Chirality : 0.042 0.238 2254 Planarity : 0.004 0.048 2595 Dihedral : 12.728 162.507 2278 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.35 % Allowed : 19.45 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1865 helix: 1.04 (0.16), residues: 986 sheet: 0.29 (0.46), residues: 134 loop : -0.38 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 40 HIS 0.004 0.001 HIS C1086 PHE 0.013 0.002 PHE B1061 TYR 0.018 0.002 TYR D 213 ARG 0.011 0.000 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 867 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7146 (ptm) REVERT: A 881 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.6863 (tmt170) REVERT: A 888 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6809 (mm-40) REVERT: A 976 ARG cc_start: 0.6541 (ptt-90) cc_final: 0.6019 (ptp90) REVERT: A 996 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6143 (mt0) REVERT: A 1009 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6764 (mm-30) REVERT: B 851 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: B 864 LYS cc_start: 0.7425 (mttp) cc_final: 0.7146 (tttp) REVERT: B 888 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6759 (mm-40) REVERT: B 948 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7468 (tttt) REVERT: B 965 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7904 (ttmm) REVERT: B 1089 ASP cc_start: 0.7364 (p0) cc_final: 0.6927 (p0) REVERT: C 996 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7114 (mt0) REVERT: D 103 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6818 (pttm) REVERT: D 107 ILE cc_start: 0.7949 (mt) cc_final: 0.7563 (mm) REVERT: D 121 VAL cc_start: 0.8059 (t) cc_final: 0.7643 (p) REVERT: D 230 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7716 (ttmt) REVERT: D 313 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6422 (tm-30) REVERT: D 327 MET cc_start: 0.7793 (mtm) cc_final: 0.7381 (mtm) REVERT: D 820 THR cc_start: 0.8226 (m) cc_final: 0.7990 (t) REVERT: D 835 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.6086 (mtm110) REVERT: D 848 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6021 (ptt-90) REVERT: D 864 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6952 (tmtm) REVERT: D 978 LYS cc_start: 0.6197 (mtmm) cc_final: 0.5661 (mtmt) outliers start: 36 outliers final: 18 residues processed: 207 average time/residue: 1.6503 time to fit residues: 369.1870 Evaluate side-chains 210 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 851 GLU Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 835 ARG Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN A1058 ASN C 975 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15136 Z= 0.309 Angle : 0.594 10.446 20502 Z= 0.303 Chirality : 0.045 0.242 2254 Planarity : 0.004 0.049 2595 Dihedral : 12.651 161.251 2278 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.81 % Allowed : 19.32 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1865 helix: 1.06 (0.16), residues: 978 sheet: 0.20 (0.45), residues: 138 loop : -0.33 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 40 HIS 0.005 0.001 HIS C1086 PHE 0.014 0.002 PHE D1061 TYR 0.020 0.002 TYR D 213 ARG 0.011 0.001 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 835 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5436 (mpp-170) REVERT: A 867 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6936 (ptm) REVERT: A 888 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6823 (mm-40) REVERT: A 976 ARG cc_start: 0.6572 (ptt-90) cc_final: 0.6118 (ptm-80) REVERT: A 996 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6144 (mt0) REVERT: B 851 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: B 864 LYS cc_start: 0.7375 (mttp) cc_final: 0.7068 (tttp) REVERT: B 888 GLN cc_start: 0.6991 (mm-40) cc_final: 0.6240 (mp10) REVERT: B 891 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7308 (mt-10) REVERT: B 948 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7485 (tttt) REVERT: B 965 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7898 (ttmm) REVERT: B 1089 ASP cc_start: 0.7358 (p0) cc_final: 0.6986 (p0) REVERT: C 866 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: C 996 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: C 1050 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: D 103 LYS cc_start: 0.7474 (mtmm) cc_final: 0.6855 (pttm) REVERT: D 107 ILE cc_start: 0.7963 (mt) cc_final: 0.7581 (mm) REVERT: D 121 VAL cc_start: 0.8057 (t) cc_final: 0.7647 (p) REVERT: D 230 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7658 (ttmt) REVERT: D 278 MET cc_start: 0.7576 (mtp) cc_final: 0.6948 (ttm) REVERT: D 308 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7481 (p) REVERT: D 313 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6409 (tm-30) REVERT: D 327 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7383 (mtm) REVERT: D 820 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.8016 (t) REVERT: D 848 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.5912 (ptt-90) REVERT: D 864 LYS cc_start: 0.7346 (mtpt) cc_final: 0.6981 (tmtm) REVERT: D 978 LYS cc_start: 0.6237 (mtmm) cc_final: 0.5739 (mtmt) outliers start: 43 outliers final: 20 residues processed: 207 average time/residue: 1.6610 time to fit residues: 371.7116 Evaluate side-chains 212 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 851 GLU Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN C 975 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15136 Z= 0.321 Angle : 0.604 10.955 20502 Z= 0.307 Chirality : 0.046 0.245 2254 Planarity : 0.004 0.048 2595 Dihedral : 12.631 159.815 2278 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.87 % Allowed : 19.13 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1865 helix: 1.02 (0.16), residues: 980 sheet: 0.20 (0.45), residues: 138 loop : -0.30 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 40 HIS 0.005 0.001 HIS C1086 PHE 0.014 0.002 PHE D1061 TYR 0.020 0.002 TYR D 213 ARG 0.012 0.001 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 867 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6952 (ptm) REVERT: A 888 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: A 976 ARG cc_start: 0.6554 (ptt-90) cc_final: 0.6308 (ptt-90) REVERT: A 996 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: B 851 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: B 864 LYS cc_start: 0.7370 (mttp) cc_final: 0.7072 (tttp) REVERT: B 888 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6327 (mp10) REVERT: B 948 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7491 (tttt) REVERT: B 965 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7904 (ttmm) REVERT: B 1089 ASP cc_start: 0.7357 (p0) cc_final: 0.6988 (p0) REVERT: C 866 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: C 996 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: C 1050 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: D 103 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6844 (pttm) REVERT: D 107 ILE cc_start: 0.7944 (mt) cc_final: 0.7559 (mm) REVERT: D 121 VAL cc_start: 0.8065 (t) cc_final: 0.7653 (p) REVERT: D 230 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7641 (ttmt) REVERT: D 278 MET cc_start: 0.7697 (mtp) cc_final: 0.7064 (ttm) REVERT: D 313 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6471 (tm-30) REVERT: D 327 MET cc_start: 0.7782 (mtm) cc_final: 0.7405 (mtm) REVERT: D 504 MET cc_start: 0.7986 (tpp) cc_final: 0.7610 (tpp) REVERT: D 820 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8003 (t) REVERT: D 848 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.5914 (ptt-90) REVERT: D 864 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6916 (tmtm) REVERT: D 881 ARG cc_start: 0.7711 (ttt-90) cc_final: 0.7498 (ttt-90) REVERT: D 978 LYS cc_start: 0.6277 (mtmm) cc_final: 0.5777 (mtmt) outliers start: 44 outliers final: 26 residues processed: 211 average time/residue: 1.7108 time to fit residues: 390.6901 Evaluate side-chains 214 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 851 GLU Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN C 975 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15136 Z= 0.322 Angle : 0.608 11.636 20502 Z= 0.309 Chirality : 0.046 0.245 2254 Planarity : 0.004 0.047 2595 Dihedral : 12.569 158.794 2278 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 18.99 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1865 helix: 1.03 (0.16), residues: 981 sheet: 0.19 (0.45), residues: 138 loop : -0.29 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 40 HIS 0.005 0.001 HIS C1086 PHE 0.014 0.002 PHE D1061 TYR 0.020 0.002 TYR D 213 ARG 0.011 0.001 ARG D 881 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 175 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 867 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6965 (ptm) REVERT: A 881 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.6923 (tmt170) REVERT: A 888 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: A 976 ARG cc_start: 0.6578 (ptt-90) cc_final: 0.6323 (ptt-90) REVERT: A 996 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6143 (mt0) REVERT: A 1009 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6891 (mm-30) REVERT: B 851 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: B 864 LYS cc_start: 0.7357 (mttp) cc_final: 0.7072 (tttp) REVERT: B 948 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7491 (tttt) REVERT: B 965 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7904 (ttmm) REVERT: B 1089 ASP cc_start: 0.7364 (p0) cc_final: 0.6996 (p0) REVERT: C 866 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: C 996 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: C 1050 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: D 103 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6849 (pttm) REVERT: D 107 ILE cc_start: 0.7983 (mt) cc_final: 0.7711 (mm) REVERT: D 121 VAL cc_start: 0.8081 (t) cc_final: 0.7674 (p) REVERT: D 230 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7652 (ttmt) REVERT: D 278 MET cc_start: 0.7703 (mtp) cc_final: 0.7069 (ttm) REVERT: D 313 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6451 (tm-30) REVERT: D 327 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7399 (mtm) REVERT: D 820 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 848 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.5922 (ptt-90) REVERT: D 864 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6923 (tmtm) REVERT: D 978 LYS cc_start: 0.6286 (mtmm) cc_final: 0.5814 (mttt) outliers start: 44 outliers final: 28 residues processed: 203 average time/residue: 1.6760 time to fit residues: 367.0923 Evaluate side-chains 213 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 851 GLU Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 864 LYS Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 ASN B 850 GLN C 975 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 757 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15136 Z= 0.247 Angle : 0.566 10.473 20502 Z= 0.287 Chirality : 0.043 0.236 2254 Planarity : 0.004 0.048 2595 Dihedral : 12.370 157.999 2278 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.68 % Allowed : 19.26 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1865 helix: 1.13 (0.16), residues: 983 sheet: 0.22 (0.45), residues: 138 loop : -0.26 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 40 HIS 0.004 0.001 HIS C1086 PHE 0.014 0.002 PHE B1061 TYR 0.017 0.002 TYR D 213 ARG 0.009 0.001 ARG A1085 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: A 867 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7038 (ptm) REVERT: A 881 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.6895 (tmt170) REVERT: A 888 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6792 (mm-40) REVERT: A 965 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6927 (mttt) REVERT: A 976 ARG cc_start: 0.6587 (ptt-90) cc_final: 0.6325 (ptt-90) REVERT: A 996 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6148 (mt0) REVERT: A 1009 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6869 (mm-30) REVERT: B 835 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5686 (tpp-160) REVERT: B 851 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: B 864 LYS cc_start: 0.7366 (mttp) cc_final: 0.7067 (tttp) REVERT: B 948 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7458 (tttt) REVERT: B 965 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7893 (ttmm) REVERT: B 1089 ASP cc_start: 0.7353 (p0) cc_final: 0.6944 (p0) REVERT: C 823 MET cc_start: 0.6114 (ttm) cc_final: 0.5830 (ttm) REVERT: C 866 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: C 996 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: C 1050 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: D 103 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6829 (pttm) REVERT: D 107 ILE cc_start: 0.7962 (mt) cc_final: 0.7686 (mm) REVERT: D 121 VAL cc_start: 0.8060 (t) cc_final: 0.7646 (p) REVERT: D 230 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7650 (ttmt) REVERT: D 278 MET cc_start: 0.7626 (mtp) cc_final: 0.6985 (ttm) REVERT: D 313 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6467 (tm-30) REVERT: D 327 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7354 (mtm) REVERT: D 504 MET cc_start: 0.8001 (tpp) cc_final: 0.7630 (tpp) REVERT: D 820 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (t) REVERT: D 848 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.5966 (ptt-90) REVERT: D 864 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6895 (tmtm) REVERT: D 978 LYS cc_start: 0.6246 (mtmm) cc_final: 0.5753 (mtmt) outliers start: 41 outliers final: 23 residues processed: 200 average time/residue: 1.7082 time to fit residues: 369.0970 Evaluate side-chains 211 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 851 GLU Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 835 ARG Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 996 GLN Chi-restraints excluded: chain C residue 1050 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 ARG Chi-restraints excluded: chain D residue 864 LYS Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.0040 chunk 128 optimal weight: 9.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 850 GLN A 982 ASN A1020 ASN A1058 ASN C1020 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118399 restraints weight = 18390.383| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.49 r_work: 0.3223 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15136 Z= 0.142 Angle : 0.503 11.737 20502 Z= 0.253 Chirality : 0.040 0.208 2254 Planarity : 0.004 0.048 2595 Dihedral : 11.847 156.668 2278 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.83 % Allowed : 20.23 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1865 helix: 1.32 (0.16), residues: 993 sheet: 0.22 (0.45), residues: 144 loop : -0.11 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 40 HIS 0.003 0.001 HIS D 168 PHE 0.013 0.001 PHE B1061 TYR 0.009 0.001 TYR D 131 ARG 0.011 0.000 ARG A1085 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6241.15 seconds wall clock time: 111 minutes 34.96 seconds (6694.96 seconds total)