Starting phenix.real_space_refine on Tue Jun 10 05:49:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6za9_11127/06_2025/6za9_11127.cif Found real_map, /net/cci-nas-00/data/ceres_data/6za9_11127/06_2025/6za9_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_11127/06_2025/6za9_11127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6za9_11127/06_2025/6za9_11127.map" model { file = "/net/cci-nas-00/data/ceres_data/6za9_11127/06_2025/6za9_11127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6za9_11127/06_2025/6za9_11127.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.85, per 1000 atoms: 0.71 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: 4.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 0.85 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: 3.16 Time building geometry restraints manager: 3.34 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: 10.240 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.054 0.005 TRP Q 9 HIS 0.009 0.002 HIS N 168 PHE 0.031 0.003 PHE 8 63 TYR 0.031 0.003 TYR R 72 ARG 0.010 0.001 ARG N 41 Details of bonding type rmsd hydrogen bonds : bond 0.10488 ( 855) hydrogen bonds : angle 6.10661 ( 2556) covalent geometry : bond 0.01194 (11273) covalent geometry : angle 1.52886 (15116) *********************** 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 : 1.668 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: 0.8910 (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: 0.2951 time to fit residues: 138.4746 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 : 1.253 ------------------------------------------------------------------------------- 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 110 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 7 39 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.133880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116953 restraints weight = 16612.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120098 restraints weight = 8475.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122160 restraints weight = 5269.008| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2074 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 : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.00 % Allowed : 15.93 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (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 TRP 0.014 0.002 TRP Q 9 HIS 0.004 0.001 HIS M 155 PHE 0.025 0.002 PHE K 24 TYR 0.028 0.002 TYR M 150 ARG 0.005 0.001 ARG T 42 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 855) hydrogen bonds : angle 4.64506 ( 2556) covalent geometry : bond 0.00435 (11273) covalent geometry : angle 0.71525 (15116) *********************** 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 331 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 1.051 Fit side-chains REVERT: 1 48 SER cc_start: 0.8461 (t) cc_final: 0.8192 (p) REVERT: 2 66 MET cc_start: 0.7825 (mtp) cc_final: 0.7526 (mtp) REVERT: 3 31 SER cc_start: 0.8735 (m) cc_final: 0.8432 (p) REVERT: 6 47 PHE cc_start: 0.7914 (t80) cc_final: 0.7513 (t80) REVERT: 7 47 PHE cc_start: 0.8162 (t80) cc_final: 0.7958 (t80) REVERT: 7 51 ILE cc_start: 0.7947 (tp) cc_final: 0.7448 (tt) REVERT: 8 49 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7424 (m-10) REVERT: K 16 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8700 (pp) REVERT: K 87 GLU cc_start: 0.7809 (tt0) cc_final: 0.7440 (mt-10) REVERT: M 108 SER cc_start: 0.7935 (m) cc_final: 0.7527 (t) REVERT: M 109 LYS cc_start: 0.8594 (mmmt) cc_final: 0.7885 (mttt) REVERT: M 124 ASN cc_start: 0.6795 (p0) cc_final: 0.6570 (p0) REVERT: N 35 ASN cc_start: 0.8639 (m110) cc_final: 0.8125 (p0) REVERT: N 46 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6295 (mt0) REVERT: N 73 MET cc_start: 0.8681 (mmm) cc_final: 0.8455 (mmp) REVERT: N 140 MET cc_start: 0.8760 (tmm) cc_final: 0.8557 (tmm) REVERT: Q 12 MET cc_start: 0.8677 (tpp) cc_final: 0.8138 (tpt) REVERT: Q 20 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9010 (tp) REVERT: R 46 TYR cc_start: 0.8660 (t80) cc_final: 0.8424 (t80) REVERT: R 62 MET cc_start: 0.8616 (mtt) cc_final: 0.8225 (mtp) REVERT: S 85 MET cc_start: 0.7990 (mmt) cc_final: 0.7705 (mmm) REVERT: T 13 LEU cc_start: 0.8748 (tp) cc_final: 0.8536 (tp) outliers start: 54 outliers final: 25 residues processed: 311 average time/residue: 0.2023 time to fit residues: 92.4355 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 : 1.068 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118620 restraints weight = 16858.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121693 restraints weight = 8651.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123748 restraints weight = 5372.612| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11273 Z= 0.173 Angle : 0.674 11.764 15116 Z= 0.341 Chirality : 0.041 0.212 1712 Planarity : 0.005 0.054 1807 Dihedral : 16.081 165.499 1994 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.74 % Allowed : 18.98 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1340 helix: 0.87 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 23 HIS 0.004 0.001 HIS N 168 PHE 0.019 0.002 PHE 6 54 TYR 0.024 0.002 TYR R 72 ARG 0.009 0.001 ARG M 111 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 855) hydrogen bonds : angle 4.36332 ( 2556) covalent geometry : bond 0.00383 (11273) covalent geometry : angle 0.67420 (15116) *********************** 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 318 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: 1 45 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7659 (tp40) REVERT: 2 15 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8175 (p) REVERT: 2 25 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7586 (pt) REVERT: 2 72 LEU cc_start: 0.8577 (tp) cc_final: 0.8173 (tp) REVERT: 3 31 SER cc_start: 0.8735 (m) cc_final: 0.8452 (p) REVERT: 3 66 MET cc_start: 0.6178 (ppp) cc_final: 0.4993 (mmp) REVERT: 6 47 PHE cc_start: 0.7875 (t80) cc_final: 0.7477 (t80) REVERT: 7 51 ILE cc_start: 0.8046 (tp) cc_final: 0.7574 (tt) REVERT: 8 46 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7855 (mp) REVERT: 8 49 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: K 16 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8700 (pp) REVERT: K 19 GLU cc_start: 0.7978 (tp30) cc_final: 0.7708 (tp30) REVERT: K 28 LYS cc_start: 0.8296 (mptm) cc_final: 0.7414 (mmmt) REVERT: K 87 GLU cc_start: 0.7719 (tt0) cc_final: 0.7383 (mt-10) REVERT: K 114 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7105 (tt0) REVERT: M 116 GLU cc_start: 0.8097 (tp30) cc_final: 0.7828 (tp30) REVERT: N 14 MET cc_start: 0.7853 (tpp) cc_final: 0.7605 (tpt) REVERT: N 43 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8903 (mp) REVERT: N 46 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6140 (mt0) REVERT: N 133 THR cc_start: 0.8457 (m) cc_final: 0.8166 (p) REVERT: Q 12 MET cc_start: 0.8590 (tpp) cc_final: 0.8131 (tpt) REVERT: R 62 MET cc_start: 0.8544 (mtt) cc_final: 0.8219 (mtp) REVERT: T 13 LEU cc_start: 0.8727 (tp) cc_final: 0.8518 (tp) REVERT: T 70 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2813 (mt) outliers start: 62 outliers final: 29 residues processed: 300 average time/residue: 0.2516 time to fit residues: 111.6128 Evaluate side-chains 273 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 2 residue 15 THR 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 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 49 TYR Chi-restraints excluded: chain K residue 16 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 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 P residue 11 ILE Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain S residue 50 ILE 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 34 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117531 restraints weight = 16558.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120623 restraints weight = 8342.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122589 restraints weight = 5170.782| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11273 Z= 0.200 Angle : 0.695 11.432 15116 Z= 0.349 Chirality : 0.042 0.207 1712 Planarity : 0.005 0.055 1807 Dihedral : 15.516 164.666 1994 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.20 % Allowed : 21.76 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1340 helix: 1.20 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -2.08 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 25 HIS 0.005 0.001 HIS N 168 PHE 0.019 0.002 PHE 8 63 TYR 0.025 0.002 TYR R 72 ARG 0.006 0.001 ARG M 111 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 855) hydrogen bonds : angle 4.29442 ( 2556) covalent geometry : bond 0.00458 (11273) covalent geometry : angle 0.69511 (15116) *********************** 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 315 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 1.997 Fit side-chains REVERT: 2 15 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (p) REVERT: 2 60 MET cc_start: 0.6900 (mmm) cc_final: 0.6582 (mmp) REVERT: 2 72 LEU cc_start: 0.8494 (tp) cc_final: 0.8107 (tp) REVERT: 3 31 SER cc_start: 0.8677 (m) cc_final: 0.8436 (p) REVERT: 3 66 MET cc_start: 0.6258 (ppp) cc_final: 0.5149 (mmp) REVERT: 4 39 ASN cc_start: 0.8047 (p0) cc_final: 0.7645 (p0) REVERT: 4 43 LYS cc_start: 0.8551 (tttt) cc_final: 0.8326 (tttp) REVERT: 6 47 PHE cc_start: 0.7958 (t80) cc_final: 0.7548 (t80) REVERT: 7 51 ILE cc_start: 0.8117 (tp) cc_final: 0.7723 (tp) REVERT: 8 46 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7997 (mp) REVERT: K 16 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8734 (pp) REVERT: K 19 GLU cc_start: 0.8129 (tp30) cc_final: 0.7927 (tp30) REVERT: K 28 LYS cc_start: 0.8348 (mptm) cc_final: 0.7423 (mmmt) REVERT: K 87 GLU cc_start: 0.7742 (tt0) cc_final: 0.7407 (mt-10) REVERT: M 116 GLU cc_start: 0.8121 (tp30) cc_final: 0.7839 (tp30) REVERT: N 43 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8888 (mp) REVERT: N 46 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.5852 (mp10) REVERT: Q 12 MET cc_start: 0.8632 (tpp) cc_final: 0.8036 (tpp) REVERT: R 62 MET cc_start: 0.8563 (mtt) cc_final: 0.8274 (mtp) REVERT: S 32 TYR cc_start: 0.7700 (t80) cc_final: 0.7487 (t80) REVERT: T 51 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5310 (ppp-140) outliers start: 67 outliers final: 42 residues processed: 297 average time/residue: 0.2887 time to fit residues: 124.5727 Evaluate side-chains 287 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 15 THR 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 78 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE 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 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 12 PHE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 11 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 70 VAL 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 105 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.136756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120788 restraints weight = 16281.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124014 restraints weight = 8010.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126131 restraints weight = 4857.001| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11273 Z= 0.148 Angle : 0.633 8.339 15116 Z= 0.316 Chirality : 0.039 0.159 1712 Planarity : 0.005 0.059 1807 Dihedral : 14.906 138.200 1994 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.28 % Allowed : 23.24 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1340 helix: 1.43 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.93 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 25 HIS 0.003 0.001 HIS N 61 PHE 0.015 0.001 PHE 6 54 TYR 0.022 0.002 TYR R 72 ARG 0.004 0.000 ARG N 41 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 855) hydrogen bonds : angle 4.17011 ( 2556) covalent geometry : bond 0.00320 (11273) covalent geometry : angle 0.63318 (15116) *********************** 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 308 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: 2 60 MET cc_start: 0.6846 (mmm) cc_final: 0.6526 (mmp) REVERT: 2 72 LEU cc_start: 0.8456 (tp) cc_final: 0.8093 (tp) REVERT: 3 66 MET cc_start: 0.6241 (ppp) cc_final: 0.5025 (mmp) REVERT: 4 39 ASN cc_start: 0.7822 (p0) cc_final: 0.7439 (p0) REVERT: 4 43 LYS cc_start: 0.8595 (tttt) cc_final: 0.8194 (tttp) REVERT: 5 45 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5868 (tt0) REVERT: 6 47 PHE cc_start: 0.7869 (t80) cc_final: 0.7457 (t80) REVERT: 7 51 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7672 (tp) REVERT: 7 56 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7394 (mp) REVERT: 7 60 MET cc_start: 0.6727 (tpp) cc_final: 0.6472 (tpp) REVERT: 7 71 ILE cc_start: 0.8462 (tt) cc_final: 0.8179 (tt) REVERT: 8 46 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8072 (mp) REVERT: K 28 LYS cc_start: 0.8404 (mptm) cc_final: 0.7451 (mmmt) REVERT: K 87 GLU cc_start: 0.7829 (tt0) cc_final: 0.7467 (mt-10) REVERT: N 43 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8847 (mp) REVERT: N 46 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.5859 (mp10) REVERT: Q 4 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8227 (mt) REVERT: Q 12 MET cc_start: 0.8611 (tpp) cc_final: 0.8170 (tpt) REVERT: T 51 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5307 (ppp-140) outliers start: 57 outliers final: 32 residues processed: 289 average time/residue: 0.2041 time to fit residues: 86.3072 Evaluate side-chains 274 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 51 ILE Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 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 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 11 ILE Chi-restraints excluded: chain Q residue 4 LEU 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 93 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 45 GLN N 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123673 restraints weight = 16763.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126553 restraints weight = 8608.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128512 restraints weight = 5335.182| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11273 Z= 0.149 Angle : 0.623 8.434 15116 Z= 0.311 Chirality : 0.039 0.191 1712 Planarity : 0.004 0.058 1807 Dihedral : 14.532 131.089 1994 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.83 % Allowed : 24.72 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1340 helix: 1.62 (0.16), residues: 1042 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 23 HIS 0.003 0.001 HIS N 168 PHE 0.020 0.001 PHE 4 63 TYR 0.023 0.001 TYR R 72 ARG 0.003 0.000 ARG N 41 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 855) hydrogen bonds : angle 4.10249 ( 2556) covalent geometry : bond 0.00325 (11273) covalent geometry : angle 0.62316 (15116) *********************** 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 305 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: 2 60 MET cc_start: 0.6768 (mmm) cc_final: 0.6486 (mmp) REVERT: 2 72 LEU cc_start: 0.8500 (tp) cc_final: 0.8117 (tp) REVERT: 3 66 MET cc_start: 0.6204 (ppp) cc_final: 0.4946 (mmp) REVERT: 4 39 ASN cc_start: 0.7699 (p0) cc_final: 0.7301 (p0) REVERT: 6 47 PHE cc_start: 0.7854 (t80) cc_final: 0.7436 (t80) REVERT: 7 51 ILE cc_start: 0.8083 (tp) cc_final: 0.7548 (tt) REVERT: 7 60 MET cc_start: 0.6884 (tpp) cc_final: 0.6573 (tpp) REVERT: 7 71 ILE cc_start: 0.8419 (tt) cc_final: 0.8125 (tt) REVERT: 8 46 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8128 (mp) REVERT: 8 62 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7669 (tt) REVERT: K 28 LYS cc_start: 0.8384 (mptm) cc_final: 0.8030 (mttm) REVERT: K 87 GLU cc_start: 0.7797 (tt0) cc_final: 0.7432 (mt-10) REVERT: K 92 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8117 (tm-30) REVERT: N 43 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8950 (mp) REVERT: N 46 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.5801 (mp10) REVERT: N 73 MET cc_start: 0.8513 (mmp) cc_final: 0.8246 (mmp) REVERT: N 149 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8124 (tp) REVERT: Q 4 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8190 (mt) REVERT: Q 12 MET cc_start: 0.8518 (tpp) cc_final: 0.8097 (tpt) REVERT: T 51 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.5240 (ppp-140) outliers start: 63 outliers final: 38 residues processed: 284 average time/residue: 0.2112 time to fit residues: 87.2096 Evaluate side-chains 281 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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 67 VAL 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 41 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 4 LEU 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 13 LEU 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 83 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120849 restraints weight = 16668.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124148 restraints weight = 8088.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126164 restraints weight = 4863.526| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11273 Z= 0.159 Angle : 0.653 10.070 15116 Z= 0.321 Chirality : 0.040 0.171 1712 Planarity : 0.004 0.058 1807 Dihedral : 14.331 124.035 1994 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.83 % Allowed : 25.09 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1340 helix: 1.67 (0.16), residues: 1046 sheet: None (None), residues: 0 loop : -1.83 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 23 HIS 0.006 0.001 HIS N 61 PHE 0.019 0.001 PHE 7 54 TYR 0.022 0.001 TYR R 72 ARG 0.004 0.000 ARG R 27 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 855) hydrogen bonds : angle 4.09894 ( 2556) covalent geometry : bond 0.00356 (11273) covalent geometry : angle 0.65313 (15116) *********************** 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 312 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 1.312 Fit side-chains REVERT: 2 60 MET cc_start: 0.6857 (mmm) cc_final: 0.6601 (mmp) REVERT: 2 72 LEU cc_start: 0.8431 (tp) cc_final: 0.8054 (tp) REVERT: 3 66 MET cc_start: 0.6237 (ppp) cc_final: 0.4950 (mmp) REVERT: 4 39 ASN cc_start: 0.7896 (p0) cc_final: 0.7368 (p0) REVERT: 6 47 PHE cc_start: 0.7862 (t80) cc_final: 0.7383 (t80) REVERT: 7 60 MET cc_start: 0.6905 (tpp) cc_final: 0.6656 (tpp) REVERT: 7 71 ILE cc_start: 0.8399 (tt) cc_final: 0.8115 (tt) REVERT: 8 46 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8202 (mp) REVERT: 8 62 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7625 (tt) REVERT: K 19 GLU cc_start: 0.7938 (tp30) cc_final: 0.7139 (tm-30) REVERT: K 87 GLU cc_start: 0.7857 (tt0) cc_final: 0.7484 (mt-10) REVERT: K 92 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8143 (tm-30) REVERT: M 107 GLN cc_start: 0.7502 (pt0) cc_final: 0.6991 (pt0) REVERT: N 43 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8921 (mp) REVERT: N 46 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.5812 (mp10) REVERT: N 73 MET cc_start: 0.8509 (mmp) cc_final: 0.8234 (mmp) REVERT: Q 12 MET cc_start: 0.8543 (tpp) cc_final: 0.7936 (tpp) REVERT: T 51 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5351 (ppp-140) outliers start: 63 outliers final: 42 residues processed: 288 average time/residue: 0.2486 time to fit residues: 104.4361 Evaluate side-chains 285 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 69 PHE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 42 LEU Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain 8 residue 62 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 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 11 ILE 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 53 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain T residue 13 LEU 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 118 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117719 restraints weight = 16740.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120817 restraints weight = 8411.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122916 restraints weight = 5204.869| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 11273 Z= 0.199 Angle : 0.691 9.599 15116 Z= 0.345 Chirality : 0.042 0.187 1712 Planarity : 0.005 0.059 1807 Dihedral : 14.362 121.670 1994 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.11 % Allowed : 25.37 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1340 helix: 1.64 (0.16), residues: 1048 sheet: None (None), residues: 0 loop : -1.87 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 23 HIS 0.016 0.002 HIS N 61 PHE 0.022 0.002 PHE 4 63 TYR 0.025 0.002 TYR 3 49 ARG 0.002 0.000 ARG R 27 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 855) hydrogen bonds : angle 4.20667 ( 2556) covalent geometry : bond 0.00464 (11273) covalent geometry : angle 0.69078 (15116) *********************** 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 311 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 245 time to evaluate : 1.079 Fit side-chains REVERT: 2 72 LEU cc_start: 0.8472 (tp) cc_final: 0.8087 (tp) REVERT: 3 66 MET cc_start: 0.6255 (ppp) cc_final: 0.4983 (mmp) REVERT: 6 47 PHE cc_start: 0.7823 (t80) cc_final: 0.7448 (t80) REVERT: 7 51 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7550 (tt) REVERT: 8 46 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8204 (mp) REVERT: K 19 GLU cc_start: 0.7988 (tp30) cc_final: 0.7750 (tp30) REVERT: K 87 GLU cc_start: 0.7828 (tt0) cc_final: 0.7457 (mt-10) REVERT: K 92 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8121 (tm-30) REVERT: M 107 GLN cc_start: 0.7610 (pt0) cc_final: 0.7384 (pt0) REVERT: N 43 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8970 (mp) REVERT: N 46 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.5886 (mp10) REVERT: P 2 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7037 (tp) REVERT: P 13 MET cc_start: 0.8899 (mtt) cc_final: 0.8467 (mtt) REVERT: Q 12 MET cc_start: 0.8579 (tpp) cc_final: 0.7498 (tpt) REVERT: T 51 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.5359 (ppp-140) outliers start: 66 outliers final: 44 residues processed: 286 average time/residue: 0.2428 time to fit residues: 102.8133 Evaluate side-chains 292 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 66 MET 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 96 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 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 1 MET 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 13 LEU 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 71 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 45 GLN Q 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121355 restraints weight = 16459.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124659 restraints weight = 8022.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126814 restraints weight = 4830.630| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11273 Z= 0.153 Angle : 0.658 8.912 15116 Z= 0.324 Chirality : 0.040 0.169 1712 Planarity : 0.004 0.060 1807 Dihedral : 13.972 117.907 1994 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.63 % Allowed : 27.31 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1340 helix: 1.82 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 23 HIS 0.002 0.001 HIS K 8 PHE 0.022 0.001 PHE 8 54 TYR 0.024 0.001 TYR 3 49 ARG 0.003 0.000 ARG R 27 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 855) hydrogen bonds : angle 4.10985 ( 2556) covalent geometry : bond 0.00341 (11273) covalent geometry : angle 0.65813 (15116) *********************** 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 292 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: 2 72 LEU cc_start: 0.8425 (tp) cc_final: 0.8035 (tp) REVERT: 3 66 MET cc_start: 0.6209 (ppp) cc_final: 0.5007 (mmp) REVERT: 6 47 PHE cc_start: 0.7845 (t80) cc_final: 0.7384 (t80) REVERT: 7 47 PHE cc_start: 0.7922 (t80) cc_final: 0.7702 (t80) REVERT: 7 51 ILE cc_start: 0.7930 (tp) cc_final: 0.7394 (tt) REVERT: 7 71 ILE cc_start: 0.8320 (tt) cc_final: 0.8059 (tt) REVERT: 8 46 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8215 (mp) REVERT: K 19 GLU cc_start: 0.7962 (tp30) cc_final: 0.7044 (tm-30) REVERT: K 80 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7924 (mm-30) REVERT: K 87 GLU cc_start: 0.7864 (tt0) cc_final: 0.7476 (mt-10) REVERT: K 92 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8156 (tm-30) REVERT: M 107 GLN cc_start: 0.7660 (pt0) cc_final: 0.7287 (pt0) REVERT: M 111 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7853 (ttp-170) REVERT: N 43 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8937 (mp) REVERT: N 46 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.5833 (mp10) REVERT: P 13 MET cc_start: 0.8865 (mtt) cc_final: 0.8599 (mtt) REVERT: Q 12 MET cc_start: 0.8582 (tpp) cc_final: 0.8123 (tpt) REVERT: T 51 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5322 (ppp-140) REVERT: T 65 GLN cc_start: 0.3375 (OUTLIER) cc_final: 0.2657 (pp30) outliers start: 50 outliers final: 35 residues processed: 273 average time/residue: 0.2332 time to fit residues: 94.4936 Evaluate side-chains 279 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 8 residue 46 LEU Chi-restraints excluded: chain K residue 36 VAL 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 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 11 ILE Chi-restraints excluded: chain P residue 28 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 13 LEU 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 73 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119108 restraints weight = 16600.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122198 restraints weight = 8427.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124253 restraints weight = 5199.371| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11273 Z= 0.186 Angle : 0.701 9.075 15116 Z= 0.345 Chirality : 0.041 0.187 1712 Planarity : 0.005 0.057 1807 Dihedral : 13.992 117.195 1994 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.35 % Allowed : 27.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1340 helix: 1.76 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.82 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 23 HIS 0.006 0.001 HIS Q 31 PHE 0.022 0.002 PHE 2 54 TYR 0.024 0.002 TYR 3 49 ARG 0.002 0.000 ARG R 27 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 855) hydrogen bonds : angle 4.16652 ( 2556) covalent geometry : bond 0.00431 (11273) covalent geometry : angle 0.70130 (15116) ********************** 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 286 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 1.204 Fit side-chains REVERT: 2 72 LEU cc_start: 0.8498 (tp) cc_final: 0.8098 (tp) REVERT: 3 66 MET cc_start: 0.6274 (ppp) cc_final: 0.5087 (mmp) REVERT: 6 47 PHE cc_start: 0.7883 (t80) cc_final: 0.7420 (t80) REVERT: 7 51 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7812 (tt) REVERT: 7 71 ILE cc_start: 0.8364 (tt) cc_final: 0.8093 (tt) REVERT: 8 46 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8199 (mp) REVERT: K 19 GLU cc_start: 0.8029 (tp30) cc_final: 0.7113 (tm-30) REVERT: K 80 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7911 (mm-30) REVERT: K 87 GLU cc_start: 0.7818 (tt0) cc_final: 0.7426 (mt-10) REVERT: K 92 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8131 (tm-30) REVERT: M 111 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7793 (ttp-170) REVERT: N 43 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8943 (mp) REVERT: N 46 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.5863 (mp10) REVERT: N 149 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8178 (tp) REVERT: Q 12 MET cc_start: 0.8584 (tpp) cc_final: 0.8077 (tpt) REVERT: T 51 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5364 (ppp-140) REVERT: T 65 GLN cc_start: 0.3361 (OUTLIER) cc_final: 0.2616 (pp30) outliers start: 47 outliers final: 36 residues processed: 267 average time/residue: 0.2078 time to fit residues: 80.6581 Evaluate side-chains 281 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 3 residue 71 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 5 residue 57 SER Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 51 ILE Chi-restraints excluded: chain 7 residue 66 MET 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 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 1 MET 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 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 13 LEU 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 3 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119974 restraints weight = 16572.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123121 restraints weight = 8442.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125227 restraints weight = 5198.894| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3933 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= 0.172 Angle : 0.690 8.853 15116 Z= 0.338 Chirality : 0.040 0.210 1712 Planarity : 0.005 0.060 1807 Dihedral : 13.861 115.555 1994 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.44 % Allowed : 27.13 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1340 helix: 1.79 (0.16), residues: 1048 sheet: None (None), residues: 0 loop : -1.77 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 23 HIS 0.003 0.001 HIS N 168 PHE 0.022 0.001 PHE 2 54 TYR 0.024 0.002 TYR 3 49 ARG 0.002 0.000 ARG R 27 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 855) hydrogen bonds : angle 4.15646 ( 2556) covalent geometry : bond 0.00394 (11273) covalent geometry : angle 0.69008 (15116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4038.30 seconds wall clock time: 73 minutes 21.42 seconds (4401.42 seconds total)