Starting phenix.real_space_refine on Wed Mar 4 06:04:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6za9_11127/03_2026/6za9_11127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6za9_11127/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6za9_11127/03_2026/6za9_11127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6za9_11127/03_2026/6za9_11127.map" model { file = "/net/cci-nas-00/data/ceres_data/6za9_11127/03_2026/6za9_11127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6za9_11127/03_2026/6za9_11127.cif" } 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-dev-5986/lib/python3.9/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: 2.57, 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: 0.94 Conformation dependent library (CDL) restraints added in 554.6 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: 0.26 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: 1.58 Time building geometry restraints manager: 1.26 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: 6447 33.44 - 66.88: 350 66.88 - 100.32: 7 100.32 - 133.76: 1 133.76 - 167.20: 1 Dihedral angle restraints: 6806 sinusoidal: 2904 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 6803 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.250 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 17.109 167.204 4316 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 covalent geometry : bond 0.01194 (11273) covalent geometry : angle 1.52886 (15116) hydrogen bonds : bond 0.10488 ( 855) hydrogen bonds : angle 6.10661 ( 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 : 0.380 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: 0.1029 time to fit residues: 48.8228 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 : 0.315 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116956 restraints weight = 16750.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120124 restraints weight = 8525.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122232 restraints weight = 5280.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123558 restraints weight = 3774.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124507 restraints weight = 3011.198| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11273 Z= 0.195 Angle : 0.715 14.195 15116 Z= 0.366 Chirality : 0.042 0.198 1712 Planarity : 0.005 0.055 1807 Dihedral : 17.113 167.795 1994 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.09 % Allowed : 15.93 % 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: -0.74 (0.21), residues: 1340 helix: 0.10 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -2.34 (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 0.025 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 covalent geometry : bond 0.00435 (11273) covalent geometry : angle 0.71525 (15116) hydrogen bonds : bond 0.05377 ( 855) hydrogen bonds : angle 4.64505 ( 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 332 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 0.275 Fit side-chains REVERT: 1 48 SER cc_start: 0.8464 (t) cc_final: 0.8195 (p) REVERT: 2 66 MET cc_start: 0.7820 (mtp) cc_final: 0.7520 (mtp) REVERT: 3 31 SER cc_start: 0.8737 (m) cc_final: 0.8422 (p) REVERT: 6 47 PHE cc_start: 0.7930 (t80) cc_final: 0.7524 (t80) REVERT: 7 47 PHE cc_start: 0.8171 (t80) cc_final: 0.7965 (t80) REVERT: 7 51 ILE cc_start: 0.7902 (tp) cc_final: 0.7402 (tt) REVERT: 8 49 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7424 (m-10) REVERT: K 16 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8703 (pp) REVERT: K 87 GLU cc_start: 0.7797 (tt0) cc_final: 0.7430 (mt-10) REVERT: K 114 GLN cc_start: 0.6651 (mt0) cc_final: 0.6275 (tt0) REVERT: M 108 SER cc_start: 0.7943 (m) cc_final: 0.7525 (t) REVERT: M 109 LYS cc_start: 0.8560 (mmmt) cc_final: 0.7870 (mttt) REVERT: M 124 ASN cc_start: 0.6767 (p0) cc_final: 0.6533 (p0) REVERT: N 35 ASN cc_start: 0.8638 (m110) cc_final: 0.8125 (p0) REVERT: N 46 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: N 73 MET cc_start: 0.8680 (mmm) cc_final: 0.8452 (mmp) REVERT: Q 12 MET cc_start: 0.8652 (tpp) cc_final: 0.8116 (tpt) REVERT: Q 20 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8995 (tp) REVERT: R 46 TYR cc_start: 0.8667 (t80) cc_final: 0.8427 (t80) REVERT: R 62 MET cc_start: 0.8595 (mtt) cc_final: 0.8211 (mtp) REVERT: S 85 MET cc_start: 0.7982 (mmt) cc_final: 0.7697 (mmm) REVERT: T 13 LEU cc_start: 0.8747 (tp) cc_final: 0.8534 (tp) outliers start: 55 outliers final: 25 residues processed: 311 average time/residue: 0.0846 time to fit residues: 39.4602 Evaluate side-chains 273 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 6 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain S residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120815 restraints weight = 16682.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124011 restraints weight = 8365.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126130 restraints weight = 5146.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127546 restraints weight = 3648.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128418 restraints weight = 2864.185| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11273 Z= 0.150 Angle : 0.649 11.516 15116 Z= 0.326 Chirality : 0.040 0.211 1712 Planarity : 0.005 0.054 1807 Dihedral : 15.852 163.061 1994 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.09 % Allowed : 19.07 % Favored : 75.83 % 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: 0.34 (0.22), residues: 1340 helix: 0.93 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -2.19 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 111 TYR 0.023 0.001 TYR R 72 PHE 0.019 0.001 PHE 6 54 TRP 0.016 0.002 TRP R 23 HIS 0.003 0.001 HIS N 61 Details of bonding type rmsd covalent geometry : bond 0.00320 (11273) covalent geometry : angle 0.64876 (15116) hydrogen bonds : bond 0.04998 ( 855) hydrogen bonds : angle 4.30165 ( 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 314 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: 1 45 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7540 (tp40) REVERT: 2 25 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7456 (pt) REVERT: 2 72 LEU cc_start: 0.8544 (tp) cc_final: 0.8126 (tp) REVERT: 3 31 SER cc_start: 0.8701 (m) cc_final: 0.8438 (p) REVERT: 3 66 MET cc_start: 0.6138 (ppp) cc_final: 0.4938 (mmp) REVERT: 6 47 PHE cc_start: 0.7835 (t80) cc_final: 0.7466 (t80) REVERT: 7 51 ILE cc_start: 0.7951 (tp) cc_final: 0.7499 (tt) REVERT: 7 66 MET cc_start: 0.7913 (tmm) cc_final: 0.7341 (tmm) REVERT: 8 49 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: K 19 GLU cc_start: 0.7920 (tp30) cc_final: 0.7659 (tp30) REVERT: K 28 LYS cc_start: 0.8284 (mptm) cc_final: 0.7389 (mmmt) REVERT: K 87 GLU cc_start: 0.7732 (tt0) cc_final: 0.7381 (mt-10) REVERT: K 114 GLN cc_start: 0.6547 (mt0) cc_final: 0.6243 (tt0) REVERT: M 118 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7895 (tp30) REVERT: N 14 MET cc_start: 0.7537 (tpp) cc_final: 0.7263 (tpt) REVERT: N 35 ASN cc_start: 0.8547 (m110) cc_final: 0.8183 (p0) REVERT: N 43 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8889 (mp) REVERT: N 46 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6092 (mt0) REVERT: N 140 MET cc_start: 0.8649 (tmm) cc_final: 0.8359 (tmm) REVERT: Q 12 MET cc_start: 0.8529 (tpp) cc_final: 0.8038 (tpt) REVERT: R 46 TYR cc_start: 0.8635 (t80) cc_final: 0.8416 (t80) REVERT: R 62 MET cc_start: 0.8500 (mtt) cc_final: 0.8179 (mtp) REVERT: S 35 LYS cc_start: 0.8743 (tmtp) cc_final: 0.8269 (mttt) REVERT: T 70 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2627 (mt) outliers start: 55 outliers final: 24 residues processed: 298 average time/residue: 0.0892 time to fit residues: 39.4714 Evaluate side-chains 263 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 49 TYR 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 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 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 Q residue 1 MET Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 19 LEU 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: 5.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 45 GLN N 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118631 restraints weight = 16698.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121789 restraints weight = 8384.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.123836 restraints weight = 5153.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125042 restraints weight = 3679.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126080 restraints weight = 2972.210| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2999 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= 0.195 Angle : 0.685 11.243 15116 Z= 0.343 Chirality : 0.042 0.201 1712 Planarity : 0.005 0.055 1807 Dihedral : 15.411 161.929 1994 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.57 % Allowed : 20.93 % Favored : 72.50 % 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 (0.23), residues: 1340 helix: 1.23 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -2.05 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 41 TYR 0.023 0.002 TYR R 72 PHE 0.018 0.002 PHE 8 63 TRP 0.012 0.002 TRP P 25 HIS 0.004 0.001 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00445 (11273) covalent geometry : angle 0.68512 (15116) hydrogen bonds : bond 0.05113 ( 855) hydrogen bonds : angle 4.25679 ( 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 320 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 0.387 Fit side-chains REVERT: 2 60 MET cc_start: 0.6831 (mmm) cc_final: 0.6530 (mmp) REVERT: 2 72 LEU cc_start: 0.8582 (tp) cc_final: 0.8165 (tp) REVERT: 3 31 SER cc_start: 0.8704 (m) cc_final: 0.8472 (p) REVERT: 3 66 MET cc_start: 0.6115 (ppp) cc_final: 0.4971 (mmp) REVERT: 4 39 ASN cc_start: 0.7945 (p0) cc_final: 0.7544 (p0) REVERT: 4 43 LYS cc_start: 0.8579 (tttt) cc_final: 0.8359 (tttp) REVERT: 6 47 PHE cc_start: 0.7919 (t80) cc_final: 0.7518 (t80) REVERT: 7 51 ILE cc_start: 0.8119 (tp) cc_final: 0.7538 (tt) REVERT: 8 46 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7895 (mp) REVERT: K 16 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8737 (pp) REVERT: K 28 LYS cc_start: 0.8338 (mptm) cc_final: 0.7414 (mmmt) REVERT: K 87 GLU cc_start: 0.7735 (tt0) cc_final: 0.7398 (mt-10) REVERT: M 116 GLU cc_start: 0.8028 (tp30) cc_final: 0.7736 (tp30) REVERT: N 14 MET cc_start: 0.7841 (tpp) cc_final: 0.7620 (tpt) REVERT: N 43 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8835 (mp) REVERT: N 46 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.5745 (mp10) REVERT: Q 12 MET cc_start: 0.8606 (tpp) cc_final: 0.8144 (tpt) REVERT: R 46 TYR cc_start: 0.8694 (t80) cc_final: 0.8485 (t80) REVERT: R 62 MET cc_start: 0.8508 (mtt) cc_final: 0.8246 (mtp) REVERT: S 32 TYR cc_start: 0.7746 (t80) cc_final: 0.7491 (t80) REVERT: T 51 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5386 (ppp-140) outliers start: 71 outliers final: 44 residues processed: 296 average time/residue: 0.0870 time to fit residues: 38.3179 Evaluate side-chains 286 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 67 VAL 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 45 GLN 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 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 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 54 THR 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 108 SER 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 49 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119318 restraints weight = 16650.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122590 restraints weight = 8174.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124811 restraints weight = 4970.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126265 restraints weight = 3500.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127030 restraints weight = 2742.969| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11273 Z= 0.161 Angle : 0.642 10.509 15116 Z= 0.321 Chirality : 0.040 0.159 1712 Planarity : 0.005 0.058 1807 Dihedral : 14.949 139.124 1994 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.46 % Allowed : 22.69 % 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: 1.08 (0.23), residues: 1340 helix: 1.42 (0.16), residues: 1051 sheet: None (None), residues: 0 loop : -1.91 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 41 TYR 0.021 0.002 TYR R 72 PHE 0.015 0.001 PHE 6 54 TRP 0.010 0.001 TRP P 25 HIS 0.002 0.001 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00357 (11273) covalent geometry : angle 0.64243 (15116) hydrogen bonds : bond 0.04951 ( 855) hydrogen bonds : angle 4.18336 ( 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 303 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.384 Fit side-chains REVERT: 2 60 MET cc_start: 0.6900 (mmm) cc_final: 0.6594 (mmp) REVERT: 2 72 LEU cc_start: 0.8486 (tp) cc_final: 0.8119 (tp) REVERT: 3 66 MET cc_start: 0.6175 (ppp) cc_final: 0.4946 (mmp) REVERT: 4 43 LYS cc_start: 0.8579 (tttt) cc_final: 0.8193 (tttp) REVERT: 6 47 PHE cc_start: 0.7869 (t80) cc_final: 0.7469 (t80) REVERT: 7 51 ILE cc_start: 0.7998 (tp) cc_final: 0.7627 (tp) REVERT: 7 71 ILE cc_start: 0.8439 (tt) cc_final: 0.8149 (tt) REVERT: 8 46 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8072 (mp) REVERT: K 16 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8751 (pp) REVERT: K 19 GLU cc_start: 0.7994 (tp30) cc_final: 0.7017 (tm-30) REVERT: K 28 LYS cc_start: 0.8406 (mptm) cc_final: 0.7455 (mmmt) REVERT: K 87 GLU cc_start: 0.7835 (tt0) cc_final: 0.7460 (mt-10) REVERT: N 43 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8776 (mp) REVERT: N 46 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.5704 (mp10) REVERT: Q 4 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8213 (mt) REVERT: Q 12 MET cc_start: 0.8591 (tpp) cc_final: 0.8119 (tpt) REVERT: R 62 MET cc_start: 0.8590 (mtt) cc_final: 0.8274 (mtp) REVERT: S 32 TYR cc_start: 0.7784 (t80) cc_final: 0.7568 (t80) REVERT: T 51 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.5331 (ppp-140) outliers start: 59 outliers final: 39 residues processed: 285 average time/residue: 0.0838 time to fit residues: 35.6132 Evaluate side-chains 280 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 45 GLN 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 16 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 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 49 MET 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 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 1 MET Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 4 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN 5 45 GLN N 101 ASN N 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120815 restraints weight = 16519.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124079 restraints weight = 8083.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126282 restraints weight = 4913.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127543 restraints weight = 3448.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128612 restraints weight = 2752.327| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3421 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= 0.153 Angle : 0.630 8.522 15116 Z= 0.314 Chirality : 0.039 0.158 1712 Planarity : 0.004 0.058 1807 Dihedral : 14.610 131.388 1994 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.37 % Allowed : 24.72 % Favored : 69.91 % 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: 1.58 (0.16), residues: 1049 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 41 TYR 0.021 0.001 TYR R 72 PHE 0.018 0.001 PHE 6 54 TRP 0.016 0.001 TRP R 23 HIS 0.002 0.001 HIS N 61 Details of bonding type rmsd covalent geometry : bond 0.00336 (11273) covalent geometry : angle 0.62954 (15116) hydrogen bonds : bond 0.04833 ( 855) hydrogen bonds : angle 4.12623 ( 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 303 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: 2 60 MET cc_start: 0.6921 (mmm) cc_final: 0.6678 (mmp) REVERT: 2 72 LEU cc_start: 0.8484 (tp) cc_final: 0.8115 (tp) REVERT: 3 66 MET cc_start: 0.6207 (ppp) cc_final: 0.5030 (mmm) REVERT: 4 43 LYS cc_start: 0.8597 (tttt) cc_final: 0.8199 (tttp) REVERT: 4 66 MET cc_start: 0.7659 (tmm) cc_final: 0.7402 (tmm) REVERT: 6 47 PHE cc_start: 0.7867 (t80) cc_final: 0.7427 (t80) REVERT: 7 51 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7474 (tt) REVERT: 7 71 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8159 (tt) REVERT: 8 46 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8092 (mp) REVERT: 8 62 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7701 (tt) REVERT: K 19 GLU cc_start: 0.8009 (tp30) cc_final: 0.6971 (tm-30) REVERT: K 28 LYS cc_start: 0.8407 (mptm) cc_final: 0.8013 (mttm) REVERT: K 87 GLU cc_start: 0.7850 (tt0) cc_final: 0.7475 (mt-10) REVERT: K 92 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8140 (tm-30) REVERT: N 43 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8912 (mp) REVERT: N 46 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.5783 (mp10) REVERT: N 149 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8098 (tp) REVERT: Q 12 MET cc_start: 0.8557 (tpp) cc_final: 0.8119 (tpt) REVERT: R 8 LYS cc_start: 0.8595 (mptt) cc_final: 0.8287 (mmtm) REVERT: S 32 TYR cc_start: 0.7750 (t80) cc_final: 0.7532 (t80) REVERT: T 51 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5168 (ppp-140) outliers start: 58 outliers final: 32 residues processed: 282 average time/residue: 0.0920 time to fit residues: 38.0714 Evaluate side-chains 279 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 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 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 36 VAL Chi-restraints excluded: chain K residue 47 SER 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 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 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 46 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 45 GLN T 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115745 restraints weight = 16886.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118892 restraints weight = 8479.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121004 restraints weight = 5236.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122276 restraints weight = 3742.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123218 restraints weight = 2986.691| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11273 Z= 0.208 Angle : 0.688 9.113 15116 Z= 0.344 Chirality : 0.042 0.176 1712 Planarity : 0.005 0.059 1807 Dihedral : 14.703 124.782 1994 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 6.02 % Allowed : 24.63 % Favored : 69.35 % 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: 1.23 (0.23), residues: 1340 helix: 1.54 (0.16), residues: 1051 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 41 TYR 0.024 0.002 TYR R 72 PHE 0.020 0.002 PHE 4 63 TRP 0.021 0.002 TRP R 23 HIS 0.004 0.001 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00481 (11273) covalent geometry : angle 0.68758 (15116) hydrogen bonds : bond 0.05124 ( 855) hydrogen bonds : angle 4.21611 ( 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 318 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: 2 60 MET cc_start: 0.7069 (mmm) cc_final: 0.6817 (mmp) REVERT: 2 72 LEU cc_start: 0.8523 (tp) cc_final: 0.8139 (tp) REVERT: 3 66 MET cc_start: 0.6226 (ppp) cc_final: 0.4954 (mmp) REVERT: 4 43 LYS cc_start: 0.8661 (tttt) cc_final: 0.8419 (tttm) REVERT: 6 47 PHE cc_start: 0.7930 (t80) cc_final: 0.7456 (t80) REVERT: 7 60 MET cc_start: 0.6730 (tpp) cc_final: 0.6492 (tpp) REVERT: 8 46 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8230 (mp) REVERT: K 19 GLU cc_start: 0.8070 (tp30) cc_final: 0.7866 (tp30) REVERT: K 28 LYS cc_start: 0.8431 (mptm) cc_final: 0.8016 (mttm) REVERT: K 87 GLU cc_start: 0.7833 (tt0) cc_final: 0.7450 (mt-10) REVERT: K 92 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8113 (tm-30) REVERT: M 111 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7760 (ttp-170) REVERT: N 43 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8934 (mp) REVERT: N 46 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: P 2 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7152 (tp) REVERT: Q 12 MET cc_start: 0.8628 (tpp) cc_final: 0.7464 (tpt) REVERT: S 32 TYR cc_start: 0.7803 (t80) cc_final: 0.7555 (t80) REVERT: T 51 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5202 (ppp-140) outliers start: 65 outliers final: 43 residues processed: 293 average time/residue: 0.0895 time to fit residues: 38.6175 Evaluate side-chains 296 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 1 residue 48 SER 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 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 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 111 ARG Chi-restraints excluded: chain M residue 119 LEU 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 49 MET 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 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 2 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.0020 chunk 110 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119254 restraints weight = 16538.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122429 restraints weight = 8182.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124460 restraints weight = 4989.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125949 restraints weight = 3537.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126770 restraints weight = 2761.151| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11273 Z= 0.170 Angle : 0.675 13.800 15116 Z= 0.331 Chirality : 0.040 0.168 1712 Planarity : 0.004 0.059 1807 Dihedral : 14.415 121.907 1994 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.56 % Allowed : 25.74 % Favored : 68.70 % 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: 1.46 (0.23), residues: 1340 helix: 1.71 (0.16), residues: 1043 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 41 TYR 0.024 0.001 TYR 3 49 PHE 0.016 0.001 PHE 7 54 TRP 0.019 0.002 TRP R 23 HIS 0.004 0.001 HIS N 61 Details of bonding type rmsd covalent geometry : bond 0.00389 (11273) covalent geometry : angle 0.67470 (15116) hydrogen bonds : bond 0.04967 ( 855) hydrogen bonds : angle 4.15187 ( 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 305 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.387 Fit side-chains REVERT: 2 72 LEU cc_start: 0.8494 (tp) cc_final: 0.8100 (tp) REVERT: 3 66 MET cc_start: 0.6292 (ppp) cc_final: 0.5106 (mmp) REVERT: 4 43 LYS cc_start: 0.8704 (tttt) cc_final: 0.8346 (tttp) REVERT: 6 47 PHE cc_start: 0.7808 (t80) cc_final: 0.7410 (t80) REVERT: 7 51 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7496 (tt) REVERT: 7 60 MET cc_start: 0.6623 (tpp) cc_final: 0.6417 (tpp) REVERT: 8 46 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8213 (mp) REVERT: K 19 GLU cc_start: 0.8059 (tp30) cc_final: 0.7854 (tp30) REVERT: K 28 LYS cc_start: 0.8407 (mptm) cc_final: 0.8002 (mttm) REVERT: K 87 GLU cc_start: 0.7832 (tt0) cc_final: 0.7463 (mt-10) REVERT: K 92 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8106 (tm-30) REVERT: M 107 GLN cc_start: 0.7539 (pt0) cc_final: 0.7219 (pt0) REVERT: M 111 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7635 (ttp-170) REVERT: N 43 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8953 (mp) REVERT: N 46 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.5848 (mp10) REVERT: N 149 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8158 (tp) REVERT: P 2 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7129 (tp) REVERT: Q 4 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8169 (mt) REVERT: Q 12 MET cc_start: 0.8586 (tpp) cc_final: 0.8121 (tpt) REVERT: R 8 LYS cc_start: 0.8581 (mptt) cc_final: 0.8369 (mmtm) REVERT: T 51 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.5240 (ppp-140) outliers start: 60 outliers final: 41 residues processed: 283 average time/residue: 0.0879 time to fit residues: 36.7538 Evaluate side-chains 291 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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 2 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 32 ASN 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 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: 7.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115662 restraints weight = 16641.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118777 restraints weight = 8324.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120852 restraints weight = 5114.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122094 restraints weight = 3628.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123039 restraints weight = 2893.091| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 11273 Z= 0.224 Angle : 0.748 19.287 15116 Z= 0.368 Chirality : 0.043 0.196 1712 Planarity : 0.005 0.060 1807 Dihedral : 14.545 120.426 1994 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.37 % Allowed : 26.30 % 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: 1.31 (0.23), residues: 1340 helix: 1.58 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.75 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 27 TYR 0.027 0.002 TYR 3 49 PHE 0.021 0.002 PHE 4 63 TRP 0.015 0.002 TRP P 25 HIS 0.007 0.002 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00526 (11273) covalent geometry : angle 0.74775 (15116) hydrogen bonds : bond 0.05270 ( 855) hydrogen bonds : angle 4.27386 ( 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 302 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.347 Fit side-chains REVERT: 2 72 LEU cc_start: 0.8529 (tp) cc_final: 0.8132 (tp) REVERT: 3 66 MET cc_start: 0.6197 (ppp) cc_final: 0.5056 (mmp) REVERT: 6 47 PHE cc_start: 0.7911 (t80) cc_final: 0.7490 (t80) REVERT: 7 51 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7459 (tt) REVERT: 7 60 MET cc_start: 0.6615 (tpp) cc_final: 0.6399 (tpp) REVERT: 8 46 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8189 (mp) REVERT: K 87 GLU cc_start: 0.7837 (tt0) cc_final: 0.7451 (mt-10) REVERT: K 92 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8154 (tm-30) REVERT: M 107 GLN cc_start: 0.7830 (pt0) cc_final: 0.7621 (pt0) REVERT: M 111 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7763 (ttp-170) REVERT: N 43 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8945 (mp) REVERT: N 46 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.5846 (mp10) REVERT: P 2 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7181 (tp) REVERT: Q 4 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8189 (mt) REVERT: Q 12 MET cc_start: 0.8638 (tpp) cc_final: 0.7477 (tpt) REVERT: T 51 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5242 (ppp-140) REVERT: T 65 GLN cc_start: 0.3532 (OUTLIER) cc_final: 0.2739 (pp30) outliers start: 58 outliers final: 43 residues processed: 282 average time/residue: 0.0899 time to fit residues: 37.6009 Evaluate side-chains 293 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 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 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 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 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 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 150 PHE 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 2 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 11 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 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: 0.0870 chunk 74 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN 5 45 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119599 restraints weight = 16565.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122691 restraints weight = 8301.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124770 restraints weight = 5098.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126166 restraints weight = 3602.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127052 restraints weight = 2807.006| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11273 Z= 0.167 Angle : 0.675 10.349 15116 Z= 0.332 Chirality : 0.040 0.190 1712 Planarity : 0.004 0.060 1807 Dihedral : 14.204 117.759 1994 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.00 % Allowed : 27.31 % Favored : 67.69 % 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: 1.51 (0.23), residues: 1340 helix: 1.73 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 27 TYR 0.024 0.001 TYR 3 49 PHE 0.020 0.001 PHE 4 63 TRP 0.016 0.001 TRP R 23 HIS 0.002 0.001 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00382 (11273) covalent geometry : angle 0.67546 (15116) hydrogen bonds : bond 0.04967 ( 855) hydrogen bonds : angle 4.18075 ( 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 294 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.391 Fit side-chains REVERT: 2 72 LEU cc_start: 0.8513 (tp) cc_final: 0.8111 (tp) REVERT: 3 66 MET cc_start: 0.6418 (ppp) cc_final: 0.5204 (mmp) REVERT: 6 47 PHE cc_start: 0.7809 (t80) cc_final: 0.7421 (t80) REVERT: 7 51 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7458 (tt) REVERT: 7 60 MET cc_start: 0.6542 (tpp) cc_final: 0.6329 (tpp) REVERT: 8 46 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8194 (mp) REVERT: K 19 GLU cc_start: 0.8000 (tp30) cc_final: 0.7096 (tm-30) REVERT: K 87 GLU cc_start: 0.7823 (tt0) cc_final: 0.7442 (mt-10) REVERT: K 92 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8142 (tm-30) REVERT: M 111 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7505 (ttp-170) REVERT: N 43 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8948 (mp) REVERT: N 46 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.5857 (mp10) REVERT: N 149 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8166 (tp) REVERT: Q 4 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8178 (mt) REVERT: Q 12 MET cc_start: 0.8604 (tpp) cc_final: 0.8134 (tpt) REVERT: T 51 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5304 (ppp-140) REVERT: T 65 GLN cc_start: 0.3588 (OUTLIER) cc_final: 0.2765 (pp30) outliers start: 54 outliers final: 40 residues processed: 274 average time/residue: 0.0865 time to fit residues: 35.2747 Evaluate side-chains 287 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 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 150 PHE Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain Q residue 4 LEU 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 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: 0.9980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119528 restraints weight = 16656.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122755 restraints weight = 8323.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124851 restraints weight = 5080.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126106 restraints weight = 3597.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127174 restraints weight = 2862.631| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11273 Z= 0.169 Angle : 0.699 10.022 15116 Z= 0.342 Chirality : 0.041 0.181 1712 Planarity : 0.004 0.060 1807 Dihedral : 13.984 115.725 1994 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.00 % Allowed : 27.22 % 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: 1.58 (0.23), residues: 1340 helix: 1.77 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 41 TYR 0.025 0.002 TYR S 32 PHE 0.018 0.001 PHE 4 63 TRP 0.013 0.001 TRP R 23 HIS 0.002 0.001 HIS M 155 Details of bonding type rmsd covalent geometry : bond 0.00389 (11273) covalent geometry : angle 0.69881 (15116) hydrogen bonds : bond 0.04965 ( 855) hydrogen bonds : angle 4.16013 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.72 seconds wall clock time: 30 minutes 30.48 seconds (1830.48 seconds total)