Starting phenix.real_space_refine on Fri Sep 11 20:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6za9_11127/09_2026/6za9_11127.map" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.031 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 13 5.49 5 S 53 5.16 5 C 7370 2.51 5 N 1676 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11067 Number of models: 1 Model: "" Number of chains: 23 Chain: "1" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "2" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "3" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "4" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "5" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "6" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "7" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "8" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "K" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "M" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 519 Classifications: {'peptide': 60} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1734 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "O" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "P" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Q" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 701 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "S" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 673 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "2" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "N" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 92 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 237 Unusual residues: {'CDL': 2, 'LHG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "S" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Classifications: {'peptide': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.23 Number of scatterers: 11067 At special positions: 0 Unit cell: (109.283, 127.32, 132.625, 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 53 16.00 P 13 15.00 O 1955 8.00 N 1676 7.00 C 7370 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 285.1 milliseconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain '1' and resid 2 through 13 Processing helix chain '1' and resid 18 through 39 removed outlier: 3.853A pdb=" N ARG 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 13 Processing helix chain '2' and resid 18 through 39 removed outlier: 3.621A pdb=" N ARG 2 38 " --> pdb=" O ILE 2 34 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN 2 39 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 73 removed outlier: 3.860A pdb=" N LEU 2 46 " --> pdb=" O LEU 2 42 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 13 Processing helix chain '3' and resid 18 through 39 removed outlier: 3.548A pdb=" N ARG 3 38 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN 3 39 " --> pdb=" O GLY 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 73 removed outlier: 3.505A pdb=" N LEU 3 46 " --> pdb=" O LEU 3 42 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 13 Processing helix chain '4' and resid 18 through 39 removed outlier: 3.670A pdb=" N ARG 4 38 " --> pdb=" O ILE 4 34 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN 4 39 " --> pdb=" O GLY 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 13 Processing helix chain '5' and resid 18 through 39 removed outlier: 3.767A pdb=" N ARG 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN 5 39 " --> pdb=" O GLY 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.626A pdb=" N LEU 5 46 " --> pdb=" O LEU 5 42 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 13 Processing helix chain '6' and resid 18 through 39 removed outlier: 3.750A pdb=" N ARG 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN 6 39 " --> pdb=" O GLY 6 35 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 13 Processing helix chain '7' and resid 18 through 39 removed outlier: 3.761A pdb=" N ARG 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN 7 39 " --> pdb=" O GLY 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.759A pdb=" N LEU 7 46 " --> pdb=" O LEU 7 42 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 13 Processing helix chain '8' and resid 18 through 39 removed outlier: 3.797A pdb=" N ASN 8 39 " --> pdb=" O GLY 8 35 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 73 removed outlier: 3.509A pdb=" N LEU 8 46 " --> pdb=" O LEU 8 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 30 removed outlier: 3.784A pdb=" N PHE K 22 " --> pdb=" O PRO K 18 " (cutoff:3.500A) Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 46 removed outlier: 4.481A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 73 removed outlier: 4.337A pdb=" N SER K 59 " --> pdb=" O PRO K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 119 removed outlier: 3.536A pdb=" N LEU K 85 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 124 Processing helix chain 'M' and resid 133 through 140 removed outlier: 3.796A pdb=" N PHE M 140 " --> pdb=" O LEU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 144 removed outlier: 3.683A pdb=" N LYS M 144 " --> pdb=" O PRO M 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 141 through 144' Processing helix chain 'N' and resid 18 through 26 removed outlier: 4.123A pdb=" N LEU N 22 " --> pdb=" O PRO N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 29 No H-bonds generated for 'chain 'N' and resid 27 through 29' Processing helix chain 'N' and resid 40 through 58 Processing helix chain 'N' and resid 63 through 87 removed outlier: 3.777A pdb=" N LEU N 87 " --> pdb=" O ASN N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 removed outlier: 3.806A pdb=" N THR N 96 " --> pdb=" O THR N 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 93 through 96' Processing helix chain 'N' and resid 97 through 120 removed outlier: 3.594A pdb=" N ASN N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Proline residue: N 107 - end of helix Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 150 Processing helix chain 'N' and resid 151 through 185 Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'O' and resid 23 through 49 removed outlier: 3.534A pdb=" N SER O 49 " --> pdb=" O PHE O 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 9 Processing helix chain 'P' and resid 13 through 18 Processing helix chain 'P' and resid 21 through 52 Processing helix chain 'Q' and resid 1 through 5 removed outlier: 4.046A pdb=" N ASP Q 5 " --> pdb=" O PRO Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 20 removed outlier: 3.751A pdb=" N VAL Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 30 Processing helix chain 'R' and resid 11 through 15 removed outlier: 3.539A pdb=" N VAL R 15 " --> pdb=" O LEU R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 27 Processing helix chain 'R' and resid 30 through 50 Processing helix chain 'R' and resid 57 through 79 Processing helix chain 'R' and resid 80 through 83 Processing helix chain 'S' and resid 20 through 38 Proline residue: S 25 - end of helix removed outlier: 3.829A pdb=" N TYR S 33 " --> pdb=" O THR S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 62 Processing helix chain 'S' and resid 69 through 96 Processing helix chain 'T' and resid 8 through 70 Proline residue: T 35 - end of helix removed outlier: 3.565A pdb=" N LEU T 70 " --> pdb=" O GLU T 66 " (cutoff:3.500A) 855 hydrogen bonds defined for protein. 2556 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1729 1.32 - 1.45: 2879 1.45 - 1.57: 6544 1.57 - 1.69: 26 1.69 - 1.82: 95 Bond restraints: 11273 Sorted by residual: bond pdb=" C13 S12 T 201 " pdb=" C14 S12 T 201 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C38 CDL R 301 " pdb=" C39 CDL R 301 " ideal model delta sigma weight residual 1.517 1.313 0.204 2.70e-02 1.37e+03 5.73e+01 bond pdb=" C61 CDL R 302 " pdb=" C62 CDL R 302 " ideal model delta sigma weight residual 1.517 1.314 0.203 2.70e-02 1.37e+03 5.67e+01 bond pdb=" C41 CDL R 301 " pdb=" C42 CDL R 301 " ideal model delta sigma weight residual 1.517 1.315 0.202 2.70e-02 1.37e+03 5.62e+01 bond pdb=" C58 CDL N 401 " pdb=" C59 CDL N 401 " ideal model delta sigma weight residual 1.517 1.315 0.202 2.70e-02 1.37e+03 5.59e+01 ... (remaining 11268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 14362 2.74 - 5.48: 523 5.48 - 8.22: 121 8.22 - 10.96: 53 10.96 - 13.70: 57 Bond angle restraints: 15116 Sorted by residual: angle pdb=" CB3 CDL R 301 " pdb=" OB5 CDL R 301 " pdb=" PB2 CDL R 301 " ideal model delta sigma weight residual 121.27 129.03 -7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" CA3 CDL N 401 " pdb=" OA5 CDL N 401 " pdb=" PA1 CDL N 401 " ideal model delta sigma weight residual 121.27 128.13 -6.86 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA2 CDL R 301 " pdb=" OA2 CDL R 301 " pdb=" PA1 CDL R 301 " ideal model delta sigma weight residual 121.27 128.07 -6.80 1.00e+00 1.00e+00 4.62e+01 angle pdb=" CB3 CDL N 401 " pdb=" OB5 CDL N 401 " pdb=" PB2 CDL N 401 " ideal model delta sigma weight residual 121.27 127.27 -6.00 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA3 CDL R 302 " pdb=" OA5 CDL R 302 " pdb=" PA1 CDL R 302 " ideal model delta sigma weight residual 121.27 127.09 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 15111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 6389 33.44 - 66.88: 275 66.88 - 100.32: 3 100.32 - 133.76: 0 133.76 - 167.20: 1 Dihedral angle restraints: 6668 sinusoidal: 2766 harmonic: 3902 Sorted by residual: dihedral pdb=" CA GLY O 14 " pdb=" C GLY O 14 " pdb=" N ILE O 15 " pdb=" CA ILE O 15 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE N 147 " pdb=" C ILE N 147 " pdb=" N SER N 148 " pdb=" CA SER N 148 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA MET Q 40 " pdb=" C MET Q 40 " pdb=" N THR Q 41 " pdb=" CA THR Q 41 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 6665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 1708 1.018 - 2.035: 0 2.035 - 3.053: 0 3.053 - 4.071: 0 4.071 - 5.088: 4 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CB4 CDL R 301 " pdb=" CB3 CDL R 301 " pdb=" CB6 CDL R 301 " pdb=" OB6 CDL R 301 " both_signs ideal model delta sigma weight residual False -2.57 2.51 -5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" CB4 CDL N 401 " pdb=" CB3 CDL N 401 " pdb=" CB6 CDL N 401 " pdb=" OB6 CDL N 401 " both_signs ideal model delta sigma weight residual False -2.57 2.37 -4.95 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" CB4 CDL R 302 " pdb=" CB3 CDL R 302 " pdb=" CB6 CDL R 302 " pdb=" OB6 CDL R 302 " both_signs ideal model delta sigma weight residual False -2.57 2.15 -4.72 2.00e-01 2.50e+01 5.57e+02 ... (remaining 1709 not shown) Planarity restraints: 1807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 S12 T 201 " -0.132 2.00e-02 2.50e+03 2.27e-01 5.17e+02 pdb=" C13 S12 T 201 " 0.293 2.00e-02 2.50e+03 pdb=" C14 S12 T 201 " -0.293 2.00e-02 2.50e+03 pdb=" C15 S12 T 201 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG K 301 " 0.127 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C8 LHG K 301 " -0.037 2.00e-02 2.50e+03 pdb=" O7 LHG K 301 " -0.039 2.00e-02 2.50e+03 pdb=" O9 LHG K 301 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG 2 101 " 0.102 2.00e-02 2.50e+03 5.89e-02 3.46e+01 pdb=" C8 LHG 2 101 " -0.030 2.00e-02 2.50e+03 pdb=" O7 LHG 2 101 " -0.031 2.00e-02 2.50e+03 pdb=" O9 LHG 2 101 " -0.041 2.00e-02 2.50e+03 ... (remaining 1804 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2606 2.78 - 3.31: 10376 3.31 - 3.84: 18880 3.84 - 4.37: 20997 4.37 - 4.90: 36187 Nonbonded interactions: 89046 Sorted by model distance: nonbonded pdb=" O GLY N 111 " pdb=" OG1 THR N 115 " model vdw 2.254 3.040 nonbonded pdb=" O2 LHG S 202 " pdb=" O3 LHG S 202 " model vdw 2.264 2.432 nonbonded pdb=" OH TYR K 26 " pdb=" O PRO T 3 " model vdw 2.283 3.040 nonbonded pdb=" O ASN S 58 " pdb=" OG1 THR S 62 " model vdw 2.290 3.040 nonbonded pdb=" O6 LHG S 201 " pdb=" O7 LHG S 201 " model vdw 2.292 2.432 ... (remaining 89041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = (chain '2' and resid 1 through 74) selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.012 0.204 11273 Z= 0.502 Angle : 1.529 13.701 15116 Z= 0.700 Chirality : 0.242 5.088 1712 Planarity : 0.010 0.227 1807 Dihedral : 15.809 167.204 4178 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.74 % Allowed : 8.24 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.17), residues: 1340 helix: -2.04 (0.12), residues: 1047 sheet: None (None), residues: 0 loop : -3.07 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 41 TYR 0.031 0.003 TYR R 72 PHE 0.031 0.003 PHE 8 63 TRP 0.054 0.005 TRP Q 9 HIS 0.009 0.002 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01194 / 0.50 (11273) covalent geometry : angle 1.52886 / 0.70 (15116) hydrogen bonds : bond 0.10488 / 7.08 ( 855) hydrogen bonds : angle 6.10661 / 4.38 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 331 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: 3 43 LYS cc_start: 0.8112 (tttt) cc_final: 0.7475 (ttpp) REVERT: 3 66 MET cc_start: 0.6756 (ttp) cc_final: 0.5505 (tpt) REVERT: 4 66 MET cc_start: 0.6587 (pp-130) cc_final: 0.4831 (mmm) REVERT: 6 47 PHE cc_start: 0.8397 (t80) cc_final: 0.7957 (t80) REVERT: 6 66 MET cc_start: 0.7776 (ttp) cc_final: 0.7571 (ttt) REVERT: 6 69 PHE cc_start: 0.8010 (m-10) cc_final: 0.7744 (t80) REVERT: 7 43 LYS cc_start: 0.7320 (tttt) cc_final: 0.7112 (tttt) REVERT: 7 47 PHE cc_start: 0.8605 (t80) cc_final: 0.8351 (t80) REVERT: 7 51 ILE cc_start: 0.8203 (tp) cc_final: 0.7940 (tt) REVERT: K 44 TYR cc_start: 0.9152 (t80) cc_final: 0.8889 (t80) REVERT: K 114 GLN cc_start: 0.6863 (mt0) cc_final: 0.6508 (mm-40) REVERT: M 109 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7927 (mttt) REVERT: M 121 LYS cc_start: 0.8175 (tmmt) cc_final: 0.7853 (tttt) REVERT: M 138 GLU cc_start: 0.8843 (tt0) cc_final: 0.8344 (tm-30) REVERT: M 152 TYR cc_start: 0.8943 (m-80) cc_final: 0.8581 (m-80) REVERT: N 35 ASN cc_start: 0.9039 (m110) cc_final: 0.8466 (p0) REVERT: N 140 MET cc_start: 0.8906 (tmm) cc_final: 0.8656 (tmm) REVERT: N 194 ILE cc_start: 0.9148 (mm) cc_final: 0.8941 (mt) REVERT: O 35 TYR cc_start: 0.7919 (m-10) cc_final: 0.7673 (m-10) REVERT: R 19 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8053 (tp30) REVERT: R 62 MET cc_start: 0.9191 (mtt) cc_final: 0.8909 (mtp) REVERT: S 35 LYS cc_start: 0.9026 (tmtp) cc_final: 0.8353 (mttt) REVERT: S 66 LYS cc_start: 0.8828 (pttt) cc_final: 0.8578 (ptmm) REVERT: S 85 MET cc_start: 0.8746 (mmt) cc_final: 0.8453 (mmm) REVERT: S 96 ARG cc_start: 0.9215 (mtm-85) cc_final: 0.7217 (tpm170) outliers start: 8 outliers final: 1 residues processed: 337 average time/residue: 0.1007 time to fit residues: 47.6760 Evaluate side-chains 241 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 39 ASN 5 39 ASN 7 39 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116961 restraints weight = 16756.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120129 restraints weight = 8516.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122214 restraints weight = 5284.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123611 restraints weight = 3793.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124285 restraints weight = 3005.557| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11273 Z= 0.194 Angle : 0.713 14.232 15116 Z= 0.365 Chirality : 0.042 0.200 1712 Planarity : 0.005 0.055 1807 Dihedral : 15.183 167.851 1856 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.19 % Allowed : 15.83 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1340 helix: 0.07 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -2.35 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 42 TYR 0.028 0.002 TYR M 150 PHE 0.023 0.002 PHE K 24 TRP 0.014 0.002 TRP Q 9 HIS 0.004 0.001 HIS M 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (11273) covalent geometry : angle 0.71321 / 0.37 (15116) hydrogen bonds : bond 0.05396 / 3.61 ( 855) hydrogen bonds : angle 4.64654 / 3.31 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.397 Fit side-chains REVERT: 2 66 MET cc_start: 0.7818 (mtp) cc_final: 0.7514 (mtp) REVERT: 3 31 SER cc_start: 0.8731 (m) cc_final: 0.8428 (p) REVERT: 6 47 PHE cc_start: 0.7924 (t80) cc_final: 0.7518 (t80) REVERT: 7 47 PHE cc_start: 0.8169 (t80) cc_final: 0.7965 (t80) REVERT: 7 51 ILE cc_start: 0.7921 (tp) cc_final: 0.7414 (tt) REVERT: 8 49 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: K 16 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8712 (pp) REVERT: K 87 GLU cc_start: 0.7794 (tt0) cc_final: 0.7432 (mt-10) REVERT: K 114 GLN cc_start: 0.6663 (mt0) cc_final: 0.6280 (tt0) REVERT: M 108 SER cc_start: 0.7930 (m) cc_final: 0.7526 (t) REVERT: M 109 LYS cc_start: 0.8576 (mmmt) cc_final: 0.7875 (mttt) REVERT: M 124 ASN cc_start: 0.6766 (p0) cc_final: 0.6527 (p0) REVERT: N 35 ASN cc_start: 0.8640 (m110) cc_final: 0.8125 (p0) REVERT: N 46 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6276 (mt0) REVERT: N 73 MET cc_start: 0.8630 (mmm) cc_final: 0.8410 (mmp) REVERT: N 140 MET cc_start: 0.8749 (tmm) cc_final: 0.8547 (tmm) REVERT: Q 12 MET cc_start: 0.8650 (tpp) cc_final: 0.8112 (tpt) REVERT: Q 20 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8996 (tp) REVERT: R 46 TYR cc_start: 0.8684 (t80) cc_final: 0.8449 (t80) REVERT: R 62 MET cc_start: 0.8594 (mtt) cc_final: 0.8210 (mtp) REVERT: S 85 MET cc_start: 0.7984 (mmt) cc_final: 0.7696 (mmm) REVERT: T 13 LEU cc_start: 0.8749 (tp) cc_final: 0.8535 (tp) outliers start: 56 outliers final: 25 residues processed: 312 average time/residue: 0.0865 time to fit residues: 40.4342 Evaluate side-chains 271 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 49 TYR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 12 PHE Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 32 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115439 restraints weight = 16979.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118673 restraints weight = 8613.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120805 restraints weight = 5346.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122048 restraints weight = 3825.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123051 restraints weight = 3089.522| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11273 Z= 0.205 Angle : 0.707 11.755 15116 Z= 0.358 Chirality : 0.043 0.219 1712 Planarity : 0.005 0.054 1807 Dihedral : 14.299 167.823 1856 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.67 % Allowed : 19.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.22), residues: 1340 helix: 0.79 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -2.22 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 111 TYR 0.025 0.002 TYR R 72 PHE 0.021 0.002 PHE 8 63 TRP 0.013 0.002 TRP P 25 HIS 0.004 0.001 HIS M 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (11273) covalent geometry : angle 0.70717 / 0.36 (15116) hydrogen bonds : bond 0.05344 / 3.57 ( 855) hydrogen bonds : angle 4.43367 / 3.15 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 25 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7533 (pt) REVERT: 2 66 MET cc_start: 0.7772 (mtp) cc_final: 0.7571 (mtp) REVERT: 2 72 LEU cc_start: 0.8549 (tp) cc_final: 0.8186 (tp) REVERT: 3 31 SER cc_start: 0.8753 (m) cc_final: 0.8428 (p) REVERT: 3 66 MET cc_start: 0.6178 (ppp) cc_final: 0.4976 (mmp) REVERT: 6 47 PHE cc_start: 0.7987 (t80) cc_final: 0.7540 (t80) REVERT: 7 51 ILE cc_start: 0.8011 (tp) cc_final: 0.7475 (tt) REVERT: 8 46 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7780 (mp) REVERT: 8 49 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: K 16 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8733 (pp) REVERT: K 19 GLU cc_start: 0.8009 (tp30) cc_final: 0.7728 (tp30) REVERT: K 28 LYS cc_start: 0.8342 (mptm) cc_final: 0.7465 (mmmt) REVERT: K 87 GLU cc_start: 0.7794 (tt0) cc_final: 0.7438 (mt-10) REVERT: M 116 GLU cc_start: 0.8165 (tp30) cc_final: 0.7905 (tp30) REVERT: M 118 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7945 (tp30) REVERT: N 14 MET cc_start: 0.7881 (tpp) cc_final: 0.7645 (tpt) REVERT: N 22 LEU cc_start: 0.9036 (mm) cc_final: 0.8830 (mt) REVERT: N 43 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8866 (mp) REVERT: N 46 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.6054 (mt0) REVERT: N 133 THR cc_start: 0.8554 (m) cc_final: 0.8226 (p) REVERT: Q 12 MET cc_start: 0.8639 (tpp) cc_final: 0.8180 (tpt) REVERT: R 62 MET cc_start: 0.8581 (mtt) cc_final: 0.8276 (mtp) REVERT: T 13 LEU cc_start: 0.8776 (tp) cc_final: 0.8572 (tp) REVERT: T 70 LEU cc_start: 0.3110 (OUTLIER) cc_final: 0.2822 (mt) outliers start: 72 outliers final: 36 residues processed: 299 average time/residue: 0.0849 time to fit residues: 38.2810 Evaluate side-chains 283 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain 8 residue 49 TYR Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 12 PHE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 45 GLN 7 39 ASN N 163 ASN N 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120887 restraints weight = 16921.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123777 restraints weight = 8762.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125698 restraints weight = 5458.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126779 restraints weight = 3914.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127615 restraints weight = 3171.087| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11273 Z= 0.170 Angle : 0.664 11.472 15116 Z= 0.332 Chirality : 0.041 0.206 1712 Planarity : 0.005 0.056 1807 Dihedral : 13.570 165.269 1856 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.93 % Allowed : 22.22 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1340 helix: 1.24 (0.16), residues: 1042 sheet: None (None), residues: 0 loop : -1.97 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 111 TYR 0.024 0.002 TYR R 72 PHE 0.017 0.001 PHE 8 63 TRP 0.014 0.002 TRP P 25 HIS 0.003 0.001 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (11273) covalent geometry : angle 0.66374 / 0.33 (15116) hydrogen bonds : bond 0.05038 / 3.37 ( 855) hydrogen bonds : angle 4.24323 / 3.01 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: 2 60 MET cc_start: 0.6943 (mmm) cc_final: 0.6641 (mmp) REVERT: 2 66 MET cc_start: 0.7778 (mtp) cc_final: 0.7549 (mtp) REVERT: 2 72 LEU cc_start: 0.8547 (tp) cc_final: 0.8156 (tp) REVERT: 3 31 SER cc_start: 0.8650 (m) cc_final: 0.8447 (p) REVERT: 3 66 MET cc_start: 0.6216 (ppp) cc_final: 0.5076 (mmp) REVERT: 4 39 ASN cc_start: 0.7856 (p0) cc_final: 0.7538 (p0) REVERT: 4 43 LYS cc_start: 0.8562 (tttt) cc_final: 0.8281 (tttp) REVERT: 6 47 PHE cc_start: 0.7887 (t80) cc_final: 0.7459 (t80) REVERT: 7 51 ILE cc_start: 0.7998 (tp) cc_final: 0.7648 (tp) REVERT: 7 71 ILE cc_start: 0.8453 (tt) cc_final: 0.8136 (tt) REVERT: 8 46 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8032 (mp) REVERT: K 19 GLU cc_start: 0.8124 (tp30) cc_final: 0.7900 (tp30) REVERT: K 28 LYS cc_start: 0.8392 (mptm) cc_final: 0.7427 (mmmt) REVERT: K 87 GLU cc_start: 0.7732 (tt0) cc_final: 0.7384 (mt-10) REVERT: M 116 GLU cc_start: 0.8075 (tp30) cc_final: 0.7762 (tp30) REVERT: N 14 MET cc_start: 0.7860 (tpp) cc_final: 0.7641 (tpt) REVERT: N 43 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8947 (mp) REVERT: N 46 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.5999 (mp10) REVERT: Q 12 MET cc_start: 0.8578 (tpp) cc_final: 0.8151 (tpt) REVERT: R 62 MET cc_start: 0.8562 (mtt) cc_final: 0.8248 (mtp) REVERT: T 51 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.5228 (ppp-140) REVERT: T 70 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2483 (mt) outliers start: 64 outliers final: 39 residues processed: 307 average time/residue: 0.0869 time to fit residues: 39.4077 Evaluate side-chains 286 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 45 GLN 5 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120753 restraints weight = 16563.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124074 restraints weight = 8171.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126218 restraints weight = 4959.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127700 restraints weight = 3522.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128514 restraints weight = 2763.908| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11273 Z= 0.147 Angle : 0.633 11.102 15116 Z= 0.315 Chirality : 0.040 0.195 1712 Planarity : 0.005 0.059 1807 Dihedral : 13.041 160.640 1856 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.46 % Allowed : 23.61 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.23), residues: 1340 helix: 1.46 (0.16), residues: 1043 sheet: None (None), residues: 0 loop : -1.80 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 41 TYR 0.022 0.001 TYR R 72 PHE 0.016 0.001 PHE 7 54 TRP 0.017 0.001 TRP R 23 HIS 0.003 0.001 HIS N 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (11273) covalent geometry : angle 0.63311 / 0.32 (15116) hydrogen bonds : bond 0.04817 / 3.22 ( 855) hydrogen bonds : angle 4.14064 / 2.94 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: 2 60 MET cc_start: 0.6904 (mmm) cc_final: 0.6590 (mmp) REVERT: 2 72 LEU cc_start: 0.8482 (tp) cc_final: 0.8122 (tp) REVERT: 3 66 MET cc_start: 0.6154 (ppp) cc_final: 0.4986 (mmm) REVERT: 4 39 ASN cc_start: 0.7764 (p0) cc_final: 0.7510 (p0) REVERT: 4 43 LYS cc_start: 0.8578 (tttt) cc_final: 0.8289 (tttp) REVERT: 4 66 MET cc_start: 0.7574 (tmm) cc_final: 0.7275 (tmm) REVERT: 6 47 PHE cc_start: 0.7916 (t80) cc_final: 0.7507 (t80) REVERT: 7 51 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7650 (tp) REVERT: 7 54 PHE cc_start: 0.8489 (t80) cc_final: 0.8177 (t80) REVERT: 7 56 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7408 (mp) REVERT: 7 71 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8131 (tt) REVERT: 8 46 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8108 (mp) REVERT: 8 62 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7632 (tt) REVERT: K 28 LYS cc_start: 0.8419 (mptm) cc_final: 0.7428 (mmmt) REVERT: K 87 GLU cc_start: 0.7830 (tt0) cc_final: 0.7461 (mt-10) REVERT: K 92 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8138 (tm-30) REVERT: N 43 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8897 (mp) REVERT: N 46 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6012 (mp10) REVERT: Q 12 MET cc_start: 0.8594 (tpp) cc_final: 0.8148 (tpt) REVERT: R 14 GLU cc_start: 0.7731 (tp30) cc_final: 0.7123 (tm-30) REVERT: R 62 MET cc_start: 0.8600 (mtt) cc_final: 0.8274 (mtp) REVERT: T 51 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5305 (ppp-140) outliers start: 59 outliers final: 32 residues processed: 292 average time/residue: 0.0852 time to fit residues: 36.9914 Evaluate side-chains 276 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 42 LEU Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain 8 residue 62 LEU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 45 GLN 5 45 GLN N 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117621 restraints weight = 16903.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120863 restraints weight = 8421.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123059 restraints weight = 5150.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124240 restraints weight = 3641.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125356 restraints weight = 2947.156| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11273 Z= 0.181 Angle : 0.665 8.680 15116 Z= 0.330 Chirality : 0.041 0.164 1712 Planarity : 0.005 0.058 1807 Dihedral : 12.798 131.275 1856 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.48 % Allowed : 25.19 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1340 helix: 1.57 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 41 TYR 0.023 0.002 TYR R 72 PHE 0.023 0.002 PHE 4 63 TRP 0.022 0.002 TRP R 23 HIS 0.003 0.001 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (11273) covalent geometry : angle 0.66499 / 0.33 (15116) hydrogen bonds : bond 0.04939 / 3.31 ( 855) hydrogen bonds : angle 4.15740 / 2.94 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 250 time to evaluate : 0.314 Fit side-chains REVERT: 2 60 MET cc_start: 0.7000 (mmm) cc_final: 0.6735 (mmp) REVERT: 2 72 LEU cc_start: 0.8479 (tp) cc_final: 0.8131 (tp) REVERT: 3 66 MET cc_start: 0.6196 (ppp) cc_final: 0.5036 (mmm) REVERT: 4 39 ASN cc_start: 0.8023 (p0) cc_final: 0.7463 (p0) REVERT: 6 47 PHE cc_start: 0.7935 (t80) cc_final: 0.7479 (t80) REVERT: 8 46 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8196 (mp) REVERT: K 19 GLU cc_start: 0.7964 (tp30) cc_final: 0.7764 (tp30) REVERT: K 28 LYS cc_start: 0.8419 (mptm) cc_final: 0.7467 (mmmt) REVERT: K 44 TYR cc_start: 0.8788 (t80) cc_final: 0.8532 (t80) REVERT: K 87 GLU cc_start: 0.7872 (tt0) cc_final: 0.7490 (mt-10) REVERT: K 92 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8139 (tm-30) REVERT: M 107 GLN cc_start: 0.7174 (pt0) cc_final: 0.6524 (pm20) REVERT: M 152 TYR cc_start: 0.9167 (m-10) cc_final: 0.8965 (m-10) REVERT: N 43 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8923 (mp) REVERT: N 46 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.5834 (mp10) REVERT: Q 12 MET cc_start: 0.8545 (tpp) cc_final: 0.7923 (tpp) REVERT: R 62 MET cc_start: 0.8605 (mtt) cc_final: 0.8307 (mtp) REVERT: T 51 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5297 (ppp-140) outliers start: 70 outliers final: 41 residues processed: 297 average time/residue: 0.0847 time to fit residues: 37.1790 Evaluate side-chains 287 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 46 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118522 restraints weight = 16613.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121646 restraints weight = 8346.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123732 restraints weight = 5106.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124787 restraints weight = 3610.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125786 restraints weight = 2936.241| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11273 Z= 0.183 Angle : 0.675 9.257 15116 Z= 0.333 Chirality : 0.041 0.167 1712 Planarity : 0.005 0.060 1807 Dihedral : 12.690 126.976 1856 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.93 % Allowed : 25.93 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1340 helix: 1.59 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 41 TYR 0.023 0.002 TYR R 72 PHE 0.014 0.001 PHE M 140 TRP 0.015 0.002 TRP R 23 HIS 0.005 0.001 HIS N 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (11273) covalent geometry : angle 0.67479 / 0.33 (15116) hydrogen bonds : bond 0.04967 / 3.34 ( 855) hydrogen bonds : angle 4.17024 / 2.96 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 0.386 Fit side-chains REVERT: 2 72 LEU cc_start: 0.8496 (tp) cc_final: 0.8139 (tp) REVERT: 3 66 MET cc_start: 0.6228 (ppp) cc_final: 0.5026 (mmm) REVERT: 6 47 PHE cc_start: 0.7906 (t80) cc_final: 0.7486 (t80) REVERT: 7 51 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7474 (tt) REVERT: 8 46 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8182 (mp) REVERT: K 28 LYS cc_start: 0.8398 (mptm) cc_final: 0.7442 (mmmt) REVERT: K 87 GLU cc_start: 0.7856 (tt0) cc_final: 0.7470 (mt-10) REVERT: K 92 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8143 (tm-30) REVERT: M 107 GLN cc_start: 0.7263 (pt0) cc_final: 0.6640 (pm20) REVERT: M 111 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7810 (ttp-170) REVERT: N 43 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8962 (mp) REVERT: N 46 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.5862 (mp10) REVERT: Q 12 MET cc_start: 0.8606 (tpp) cc_final: 0.8073 (tpt) REVERT: R 62 MET cc_start: 0.8610 (mtt) cc_final: 0.8302 (mtp) REVERT: T 51 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.5399 (ppp-140) outliers start: 64 outliers final: 43 residues processed: 291 average time/residue: 0.0860 time to fit residues: 37.3603 Evaluate side-chains 290 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 3 residue 42 LEU Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 111 ARG Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118580 restraints weight = 16660.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121764 restraints weight = 8331.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123918 restraints weight = 5095.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125099 restraints weight = 3595.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126020 restraints weight = 2884.891| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 11273 Z= 0.185 Angle : 0.681 8.604 15116 Z= 0.338 Chirality : 0.041 0.158 1712 Planarity : 0.005 0.060 1807 Dihedral : 12.528 123.055 1856 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.74 % Allowed : 26.30 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.23), residues: 1340 helix: 1.67 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 41 TYR 0.023 0.002 TYR R 72 PHE 0.016 0.001 PHE 8 54 TRP 0.013 0.001 TRP R 23 HIS 0.003 0.001 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (11273) covalent geometry : angle 0.68056 / 0.34 (15116) hydrogen bonds : bond 0.04989 / 3.35 ( 855) hydrogen bonds : angle 4.17847 / 2.96 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 0.399 Fit side-chains REVERT: 1 32 LEU cc_start: 0.8642 (tp) cc_final: 0.8430 (tp) REVERT: 2 72 LEU cc_start: 0.8499 (tp) cc_final: 0.8148 (tp) REVERT: 3 66 MET cc_start: 0.6289 (ppp) cc_final: 0.5088 (mmm) REVERT: 6 47 PHE cc_start: 0.7935 (t80) cc_final: 0.7488 (t80) REVERT: 7 51 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7427 (tt) REVERT: 8 46 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8233 (mp) REVERT: K 19 GLU cc_start: 0.8072 (tp30) cc_final: 0.6979 (tm-30) REVERT: K 28 LYS cc_start: 0.8405 (mptm) cc_final: 0.7453 (mmmt) REVERT: K 44 TYR cc_start: 0.8806 (t80) cc_final: 0.8502 (t80) REVERT: K 87 GLU cc_start: 0.7850 (tt0) cc_final: 0.7460 (mt-10) REVERT: K 92 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8129 (tm-30) REVERT: M 107 GLN cc_start: 0.7424 (pt0) cc_final: 0.7157 (pt0) REVERT: M 111 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7788 (ttp-170) REVERT: N 43 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8930 (mp) REVERT: N 46 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.5856 (mp10) REVERT: Q 12 MET cc_start: 0.8590 (tpp) cc_final: 0.8105 (tpt) REVERT: R 62 MET cc_start: 0.8601 (mtt) cc_final: 0.8307 (mtp) REVERT: T 51 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5370 (ppp-140) outliers start: 62 outliers final: 45 residues processed: 282 average time/residue: 0.0852 time to fit residues: 35.9001 Evaluate side-chains 291 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 3 residue 42 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 111 ARG Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 TYR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 56 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119446 restraints weight = 16464.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122598 restraints weight = 8283.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124693 restraints weight = 5065.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125993 restraints weight = 3577.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126996 restraints weight = 2816.263| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11273 Z= 0.173 Angle : 0.673 8.967 15116 Z= 0.332 Chirality : 0.041 0.187 1712 Planarity : 0.005 0.060 1807 Dihedral : 12.306 119.234 1856 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.65 % Allowed : 26.57 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1340 helix: 1.73 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.88 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 41 TYR 0.024 0.002 TYR 3 49 PHE 0.024 0.001 PHE 4 63 TRP 0.012 0.001 TRP R 23 HIS 0.003 0.001 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (11273) covalent geometry : angle 0.67278 / 0.33 (15116) hydrogen bonds : bond 0.04938 / 3.33 ( 855) hydrogen bonds : angle 4.15126 / 2.94 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 0.366 Fit side-chains REVERT: 2 60 MET cc_start: 0.7117 (mmm) cc_final: 0.6854 (mmp) REVERT: 2 72 LEU cc_start: 0.8506 (tp) cc_final: 0.8150 (tp) REVERT: 3 60 MET cc_start: 0.7047 (tpp) cc_final: 0.6673 (tpp) REVERT: 3 66 MET cc_start: 0.6462 (ppp) cc_final: 0.5082 (mmp) REVERT: 6 47 PHE cc_start: 0.7912 (t80) cc_final: 0.7500 (t80) REVERT: 7 51 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7475 (tt) REVERT: 8 46 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8206 (mp) REVERT: K 19 GLU cc_start: 0.8102 (tp30) cc_final: 0.7015 (tm-30) REVERT: K 87 GLU cc_start: 0.7847 (tt0) cc_final: 0.7458 (mt-10) REVERT: K 92 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8143 (tm-30) REVERT: M 126 ILE cc_start: 0.8965 (mm) cc_final: 0.8734 (mt) REVERT: N 43 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8925 (mp) REVERT: N 46 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.5846 (mp10) REVERT: N 149 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8186 (tp) REVERT: N 225 ASN cc_start: 0.8823 (p0) cc_final: 0.8616 (p0) REVERT: Q 12 MET cc_start: 0.8618 (tpp) cc_final: 0.8097 (tpt) REVERT: R 62 MET cc_start: 0.8592 (mtt) cc_final: 0.8292 (mtp) REVERT: T 51 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5420 (ppp-140) REVERT: T 65 GLN cc_start: 0.3786 (OUTLIER) cc_final: 0.2980 (pp30) outliers start: 61 outliers final: 45 residues processed: 287 average time/residue: 0.0887 time to fit residues: 37.4111 Evaluate side-chains 296 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 12 PHE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 TYR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 65 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117755 restraints weight = 16685.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120916 restraints weight = 8349.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123039 restraints weight = 5124.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124301 restraints weight = 3619.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125351 restraints weight = 2879.221| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 11273 Z= 0.193 Angle : 0.709 9.072 15116 Z= 0.349 Chirality : 0.041 0.205 1712 Planarity : 0.005 0.061 1807 Dihedral : 12.311 117.596 1856 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.09 % Allowed : 26.57 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.23), residues: 1340 helix: 1.70 (0.16), residues: 1048 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 41 TYR 0.029 0.002 TYR 3 49 PHE 0.023 0.001 PHE 4 63 TRP 0.010 0.001 TRP P 25 HIS 0.003 0.001 HIS N 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (11273) covalent geometry : angle 0.70856 / 0.35 (15116) hydrogen bonds : bond 0.04994 / 3.36 ( 855) hydrogen bonds : angle 4.20682 / 2.98 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.269 Fit side-chains REVERT: 2 60 MET cc_start: 0.7119 (mmm) cc_final: 0.6859 (mmp) REVERT: 2 72 LEU cc_start: 0.8513 (tp) cc_final: 0.8165 (tp) REVERT: 3 60 MET cc_start: 0.7023 (tpp) cc_final: 0.6679 (tpp) REVERT: 3 66 MET cc_start: 0.6259 (ppp) cc_final: 0.5051 (mmm) REVERT: 6 47 PHE cc_start: 0.7971 (t80) cc_final: 0.7545 (t80) REVERT: 7 51 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7433 (tt) REVERT: 7 71 ILE cc_start: 0.8324 (tt) cc_final: 0.8095 (tt) REVERT: 8 46 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8205 (mp) REVERT: K 19 GLU cc_start: 0.8146 (tp30) cc_final: 0.7082 (tm-30) REVERT: K 87 GLU cc_start: 0.7827 (tt0) cc_final: 0.7443 (mt-10) REVERT: K 92 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8147 (tm-30) REVERT: M 107 GLN cc_start: 0.7176 (pt0) cc_final: 0.6914 (pm20) REVERT: M 111 ARG cc_start: 0.8538 (ptp-170) cc_final: 0.8117 (ptp-170) REVERT: N 43 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8939 (mp) REVERT: N 46 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.5874 (mp10) REVERT: N 225 ASN cc_start: 0.8825 (p0) cc_final: 0.8623 (p0) REVERT: Q 12 MET cc_start: 0.8585 (tpp) cc_final: 0.8097 (tpt) REVERT: R 62 MET cc_start: 0.8635 (mtt) cc_final: 0.8328 (mtp) REVERT: T 51 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5451 (ppp-140) REVERT: T 65 GLN cc_start: 0.3771 (OUTLIER) cc_final: 0.2956 (pp30) outliers start: 55 outliers final: 45 residues processed: 277 average time/residue: 0.0817 time to fit residues: 33.6305 Evaluate side-chains 293 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 TYR Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 81 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 51 ARG Chi-restraints excluded: chain T residue 65 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 117 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120301 restraints weight = 16629.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123486 restraints weight = 8334.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125618 restraints weight = 5096.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126906 restraints weight = 3596.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127909 restraints weight = 2842.666| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11273 Z= 0.159 Angle : 0.674 9.229 15116 Z= 0.330 Chirality : 0.040 0.192 1712 Planarity : 0.004 0.059 1807 Dihedral : 12.050 115.298 1856 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.72 % Allowed : 27.41 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1340 helix: 1.79 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 41 TYR 0.026 0.001 TYR 3 49 PHE 0.024 0.001 PHE 4 63 TRP 0.012 0.001 TRP R 23 HIS 0.004 0.001 HIS N 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (11273) covalent geometry : angle 0.67432 / 0.33 (15116) hydrogen bonds : bond 0.04834 / 3.25 ( 855) hydrogen bonds : angle 4.14953 / 2.94 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.23 seconds wall clock time: 29 minutes 35.10 seconds (1775.10 seconds total)