Starting phenix.real_space_refine on Thu Sep 18 03:44:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eil_48086/09_2025/9eil_48086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eil_48086/09_2025/9eil_48086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eil_48086/09_2025/9eil_48086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eil_48086/09_2025/9eil_48086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eil_48086/09_2025/9eil_48086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eil_48086/09_2025/9eil_48086.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 283 5.49 5 S 22 5.16 5 C 7951 2.51 5 N 2636 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14070 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2904 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain: "J" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2874 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "K" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 270} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'ZSL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12877 SG CYS K 141 44.098 65.647 71.459 1.00114.38 S ATOM 12897 SG CYS K 144 43.190 68.486 69.603 1.00 89.70 S ATOM 13062 SG CYS K 166 41.380 64.971 68.847 1.00115.24 S ATOM 13140 SG CYS K 177 45.032 65.611 67.925 1.00101.68 S Time building chain proxies: 3.29, per 1000 atoms: 0.23 Number of scatterers: 14070 At special positions: 0 Unit cell: (111.22, 117.03, 127.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 22 16.00 P 283 15.00 O 3177 8.00 N 2636 7.00 C 7951 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 429.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 177 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 144 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 166 " Number of angles added : 6 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 11 sheets defined 62.0% alpha, 4.4% beta 141 base pairs and 232 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.886A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.657A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.710A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.620A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.549A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.717A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.837A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.581A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.529A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.771A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 44 removed outlier: 3.879A pdb=" N GLN K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 removed outlier: 4.154A pdb=" N SER K 59 " --> pdb=" O ILE K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 76 Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.795A pdb=" N MET K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 125 through 129 Processing helix chain 'K' and resid 170 through 174 removed outlier: 4.332A pdb=" N GLY K 173 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 207 Processing helix chain 'K' and resid 224 through 231 removed outlier: 3.596A pdb=" N LYS K 230 " --> pdb=" O PRO K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.150A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.452A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.485A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.827A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.760A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 107 through 110 removed outlier: 6.664A pdb=" N VAL K 47 " --> pdb=" O ARG K 108 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU K 110 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE K 49 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL K 48 " --> pdb=" O ILE K 211 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU K 213 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS K 50 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ILE K 254 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE K 238 " --> pdb=" O ILE K 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 147 through 149 removed outlier: 4.397A pdb=" N THR K 184 " --> pdb=" O ASN K 135 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 362 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 232 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3782 1.34 - 1.47: 4827 1.47 - 1.59: 5765 1.59 - 1.72: 486 1.72 - 1.85: 39 Bond restraints: 14899 Sorted by residual: bond pdb=" O39 ZSL A 201 " pdb=" P44 ZSL A 201 " ideal model delta sigma weight residual 1.497 1.398 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C20 ZSL A 201 " pdb=" S46 ZSL A 201 " ideal model delta sigma weight residual 1.830 1.744 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C25 ZSL A 201 " pdb=" C27 ZSL A 201 " ideal model delta sigma weight residual 1.386 1.467 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O38 ZSL A 201 " pdb=" P44 ZSL A 201 " ideal model delta sigma weight residual 1.493 1.567 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C20 ZSL A 201 " pdb=" O36 ZSL A 201 " ideal model delta sigma weight residual 1.391 1.461 -0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 14894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 21330 5.41 - 10.83: 16 10.83 - 16.24: 0 16.24 - 21.65: 1 21.65 - 27.07: 1 Bond angle restraints: 21348 Sorted by residual: angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP1 DG I 21 " ideal model delta sigma weight residual 108.00 80.93 27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP2 DG I 21 " ideal model delta sigma weight residual 108.00 87.51 20.49 3.00e+00 1.11e-01 4.66e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.44 5.09 9.80e-01 1.04e+00 2.70e+01 angle pdb=" CA PRO K 221 " pdb=" N PRO K 221 " pdb=" CD PRO K 221 " ideal model delta sigma weight residual 112.00 106.72 5.28 1.40e+00 5.10e-01 1.42e+01 angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" O5' DG I 21 " ideal model delta sigma weight residual 104.00 98.67 5.33 1.50e+00 4.44e-01 1.26e+01 ... (remaining 21343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 6955 34.74 - 69.48: 1320 69.48 - 104.22: 16 104.22 - 138.95: 0 138.95 - 173.69: 2 Dihedral angle restraints: 8293 sinusoidal: 5272 harmonic: 3021 Sorted by residual: dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.69 -173.69 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 57.34 162.66 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA LYS C 75 " pdb=" CB LYS C 75 " pdb=" CG LYS C 75 " pdb=" CD LYS C 75 " ideal model delta sinusoidal sigma weight residual -180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.421: 2430 0.421 - 0.841: 0 0.841 - 1.262: 0 1.262 - 1.682: 0 1.682 - 2.103: 1 Chirality restraints: 2431 Sorted by residual: chirality pdb=" P DG I 21 " pdb=" OP1 DG I 21 " pdb=" OP2 DG I 21 " pdb=" O5' DG I 21 " both_signs ideal model delta sigma weight residual True 2.35 0.24 2.10 2.00e-01 2.50e+01 1.11e+02 chirality pdb=" CA PRO K 221 " pdb=" N PRO K 221 " pdb=" C PRO K 221 " pdb=" CB PRO K 221 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C18 ZSL A 201 " pdb=" C17 ZSL A 201 " pdb=" N07 ZSL A 201 " pdb=" O33 ZSL A 201 " both_signs ideal model delta sigma weight residual False 2.33 2.58 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2428 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 220 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO K 221 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -53 " 0.028 2.00e-02 2.50e+03 1.14e-02 3.59e+00 pdb=" N9 DA I -53 " -0.011 2.00e-02 2.50e+03 pdb=" C8 DA I -53 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA I -53 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA I -53 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -53 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -53 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA I -53 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I -53 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA I -53 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DA I -53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " 0.024 2.00e-02 2.50e+03 1.09e-02 3.25e+00 pdb=" N9 DA I 26 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " -0.003 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 526 2.70 - 3.25: 12942 3.25 - 3.80: 26513 3.80 - 4.35: 32702 4.35 - 4.90: 47691 Nonbonded interactions: 120374 Sorted by model distance: nonbonded pdb=" O SER K 56 " pdb=" OG SER K 59 " model vdw 2.151 3.040 nonbonded pdb=" O ARG K 220 " pdb=" N SER K 222 " model vdw 2.195 3.120 nonbonded pdb=" NH1 ARG D 83 " pdb=" OP2 DG I -33 " model vdw 2.195 3.120 nonbonded pdb=" OG1 THR B 80 " pdb=" O ARG E 83 " model vdw 2.224 3.040 nonbonded pdb=" NH2 ARG K 65 " pdb=" O37 ZSL A 201 " model vdw 2.232 3.120 ... (remaining 120369 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 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.005 0.099 14904 Z= 0.219 Angle : 0.678 27.067 21354 Z= 0.369 Chirality : 0.056 2.103 2431 Planarity : 0.005 0.111 1730 Dihedral : 25.585 173.694 6343 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.82 % Favored : 96.89 % Rotamer: Outliers : 2.19 % Allowed : 7.95 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.27), residues: 1028 helix: 2.68 (0.21), residues: 603 sheet: -1.98 (0.81), residues: 36 loop : -1.59 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.014 0.001 TYR K 5 PHE 0.009 0.001 PHE D 62 TRP 0.006 0.001 TRP K 71 HIS 0.003 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00446 (14899) covalent geometry : angle 0.66863 (21348) hydrogen bonds : bond 0.10677 ( 829) hydrogen bonds : angle 3.89888 ( 2098) metal coordination : bond 0.01166 ( 4) metal coordination : angle 6.66086 ( 6) Misc. bond : bond 0.07804 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 368 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.8664 (t80) cc_final: 0.8446 (t80) REVERT: C 92 GLU cc_start: 0.8007 (mp0) cc_final: 0.7256 (mp0) REVERT: E 45 THR cc_start: 0.8003 (t) cc_final: 0.7682 (p) REVERT: E 54 TYR cc_start: 0.8485 (m-80) cc_final: 0.8032 (m-80) REVERT: F 59 LYS cc_start: 0.8882 (ttpp) cc_final: 0.8645 (tttt) REVERT: G 38 ASN cc_start: 0.7955 (m-40) cc_final: 0.7137 (m-40) REVERT: G 77 ARG cc_start: 0.7285 (ptp-110) cc_final: 0.6957 (ptm160) REVERT: G 89 ASN cc_start: 0.8502 (m-40) cc_final: 0.8153 (m110) REVERT: K 95 HIS cc_start: 0.7935 (m90) cc_final: 0.7702 (m-70) REVERT: K 109 PHE cc_start: 0.8065 (t80) cc_final: 0.7642 (t80) outliers start: 19 outliers final: 3 residues processed: 381 average time/residue: 0.1754 time to fit residues: 86.5384 Evaluate side-chains 255 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain K residue 164 ARG Chi-restraints excluded: chain K residue 266 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN D 79 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN F 93 GLN G 104 GLN H 60 ASN H 106 HIS ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 ASN K 268 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.106627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067021 restraints weight = 45112.225| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.81 r_work: 0.2925 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 14904 Z= 0.216 Angle : 0.684 27.378 21354 Z= 0.373 Chirality : 0.056 2.052 2431 Planarity : 0.006 0.104 1730 Dihedral : 29.036 171.755 4313 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.92 % Favored : 96.79 % Rotamer: Outliers : 5.18 % Allowed : 16.01 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.27), residues: 1028 helix: 2.39 (0.21), residues: 618 sheet: -1.54 (0.88), residues: 36 loop : -1.56 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 76 TYR 0.018 0.002 TYR B 88 PHE 0.019 0.001 PHE K 124 TRP 0.020 0.002 TRP K 276 HIS 0.009 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00492 (14899) covalent geometry : angle 0.67957 (21348) hydrogen bonds : bond 0.04793 ( 829) hydrogen bonds : angle 3.24570 ( 2098) metal coordination : bond 0.01399 ( 4) metal coordination : angle 4.55584 ( 6) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9251 (tt0) REVERT: B 74 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8871 (mm-30) REVERT: B 93 GLN cc_start: 0.8840 (mt0) cc_final: 0.8567 (mp10) REVERT: C 90 ASP cc_start: 0.8558 (t70) cc_final: 0.8157 (t0) REVERT: C 91 GLU cc_start: 0.8649 (pm20) cc_final: 0.8207 (pm20) REVERT: C 92 GLU cc_start: 0.8735 (mp0) cc_final: 0.7736 (mp0) REVERT: E 45 THR cc_start: 0.8028 (t) cc_final: 0.7670 (p) REVERT: E 60 LEU cc_start: 0.9375 (mt) cc_final: 0.9076 (mt) REVERT: F 59 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8505 (tttt) REVERT: F 88 TYR cc_start: 0.8494 (m-10) cc_final: 0.8213 (m-10) REVERT: G 38 ASN cc_start: 0.8177 (m-40) cc_final: 0.7866 (m-40) REVERT: G 91 GLU cc_start: 0.8333 (tp30) cc_final: 0.8053 (tp30) REVERT: H 65 ASP cc_start: 0.9163 (t70) cc_final: 0.8943 (t0) REVERT: H 73 GLU cc_start: 0.8817 (tp30) cc_final: 0.8543 (tp30) REVERT: H 80 TYR cc_start: 0.8453 (m-10) cc_final: 0.7852 (m-10) REVERT: H 90 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7432 (mm-30) REVERT: H 102 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8019 (tm-30) REVERT: K 51 THR cc_start: 0.8999 (p) cc_final: 0.8621 (t) REVERT: K 101 LEU cc_start: 0.9490 (mt) cc_final: 0.9266 (mt) REVERT: K 109 PHE cc_start: 0.8742 (t80) cc_final: 0.7806 (t80) REVERT: K 113 GLN cc_start: 0.7951 (pm20) cc_final: 0.7469 (pm20) REVERT: K 131 GLU cc_start: 0.9136 (mp0) cc_final: 0.8733 (pm20) REVERT: K 136 MET cc_start: 0.8252 (mmm) cc_final: 0.8028 (mmm) REVERT: K 147 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7725 (tm-30) REVERT: K 188 TRP cc_start: 0.8269 (m100) cc_final: 0.7944 (m100) REVERT: K 196 ASP cc_start: 0.9186 (m-30) cc_final: 0.8266 (t70) REVERT: K 210 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7506 (p) REVERT: K 257 TYR cc_start: 0.9495 (m-80) cc_final: 0.9252 (t80) REVERT: K 265 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8485 (mm) outliers start: 45 outliers final: 25 residues processed: 284 average time/residue: 0.1329 time to fit residues: 52.2203 Evaluate side-chains 254 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 79 HIS E 68 GLN K 95 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.104611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064244 restraints weight = 45124.120| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.90 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 14904 Z= 0.254 Angle : 0.687 27.369 21354 Z= 0.372 Chirality : 0.056 2.056 2431 Planarity : 0.005 0.108 1730 Dihedral : 29.265 170.142 4306 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.60 % Favored : 96.11 % Rotamer: Outliers : 5.65 % Allowed : 16.71 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1028 helix: 2.29 (0.21), residues: 618 sheet: -1.61 (0.90), residues: 36 loop : -1.56 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 205 TYR 0.012 0.002 TYR H 80 PHE 0.012 0.001 PHE A 67 TRP 0.022 0.002 TRP K 276 HIS 0.007 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00579 (14899) covalent geometry : angle 0.68288 (21348) hydrogen bonds : bond 0.04801 ( 829) hydrogen bonds : angle 3.26499 ( 2098) metal coordination : bond 0.01408 ( 4) metal coordination : angle 4.32615 ( 6) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8281 (mm-30) REVERT: B 88 TYR cc_start: 0.8772 (m-10) cc_final: 0.7516 (m-10) REVERT: B 93 GLN cc_start: 0.8627 (mt0) cc_final: 0.8345 (mp10) REVERT: C 90 ASP cc_start: 0.8403 (t70) cc_final: 0.7819 (t0) REVERT: C 91 GLU cc_start: 0.8420 (pm20) cc_final: 0.7743 (pm20) REVERT: C 92 GLU cc_start: 0.8464 (mp0) cc_final: 0.7310 (mp0) REVERT: D 80 TYR cc_start: 0.8325 (m-10) cc_final: 0.8073 (m-80) REVERT: E 45 THR cc_start: 0.8117 (t) cc_final: 0.7520 (p) REVERT: E 54 TYR cc_start: 0.8886 (m-80) cc_final: 0.8657 (m-80) REVERT: E 59 GLU cc_start: 0.8424 (pm20) cc_final: 0.7630 (pm20) REVERT: E 94 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7816 (mm-30) REVERT: E 105 GLU cc_start: 0.8271 (tt0) cc_final: 0.7842 (mt-10) REVERT: F 59 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8320 (tttt) REVERT: F 88 TYR cc_start: 0.8424 (m-10) cc_final: 0.7775 (m-10) REVERT: G 91 GLU cc_start: 0.8126 (tp30) cc_final: 0.7834 (tp30) REVERT: G 92 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7612 (mt-10) REVERT: H 65 ASP cc_start: 0.8952 (t70) cc_final: 0.8670 (t0) REVERT: H 80 TYR cc_start: 0.8150 (m-10) cc_final: 0.7660 (m-10) REVERT: K 51 THR cc_start: 0.8987 (p) cc_final: 0.8356 (t) REVERT: K 55 ILE cc_start: 0.7261 (mm) cc_final: 0.6944 (mm) REVERT: K 109 PHE cc_start: 0.8828 (t80) cc_final: 0.7797 (t80) REVERT: K 113 GLN cc_start: 0.7836 (pm20) cc_final: 0.7453 (pm20) REVERT: K 131 GLU cc_start: 0.8945 (mp0) cc_final: 0.8724 (pm20) REVERT: K 147 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7688 (tm-30) REVERT: K 196 ASP cc_start: 0.9310 (m-30) cc_final: 0.8370 (t0) REVERT: K 257 TYR cc_start: 0.9461 (OUTLIER) cc_final: 0.9224 (t80) outliers start: 49 outliers final: 35 residues processed: 269 average time/residue: 0.1287 time to fit residues: 48.2164 Evaluate side-chains 260 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 119 HIS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.102328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061574 restraints weight = 44903.660| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.88 r_work: 0.2818 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 14904 Z= 0.318 Angle : 0.721 27.441 21354 Z= 0.389 Chirality : 0.058 2.056 2431 Planarity : 0.006 0.114 1730 Dihedral : 29.475 169.151 4306 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.02 % Favored : 96.69 % Rotamer: Outliers : 4.38 % Allowed : 20.16 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1028 helix: 2.13 (0.21), residues: 610 sheet: -1.44 (0.79), residues: 43 loop : -1.55 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 280 TYR 0.016 0.002 TYR G 57 PHE 0.013 0.002 PHE K 137 TRP 0.039 0.004 TRP K 276 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00727 (14899) covalent geometry : angle 0.71877 (21348) hydrogen bonds : bond 0.05389 ( 829) hydrogen bonds : angle 3.39577 ( 2098) metal coordination : bond 0.01655 ( 4) metal coordination : angle 3.65699 ( 6) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8890 (mm-30) REVERT: B 88 TYR cc_start: 0.9118 (m-10) cc_final: 0.8900 (m-10) REVERT: C 90 ASP cc_start: 0.8673 (t70) cc_final: 0.8070 (t0) REVERT: C 91 GLU cc_start: 0.8751 (pm20) cc_final: 0.8122 (pm20) REVERT: C 92 GLU cc_start: 0.8798 (mp0) cc_final: 0.7613 (mp0) REVERT: D 102 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7946 (mm-30) REVERT: E 45 THR cc_start: 0.8086 (t) cc_final: 0.7643 (p) REVERT: E 59 GLU cc_start: 0.8692 (pm20) cc_final: 0.8464 (pm20) REVERT: E 94 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8438 (mm-30) REVERT: F 59 LYS cc_start: 0.8963 (ttpp) cc_final: 0.8631 (tttt) REVERT: F 88 TYR cc_start: 0.8796 (m-10) cc_final: 0.8265 (m-10) REVERT: G 91 GLU cc_start: 0.8470 (tp30) cc_final: 0.8176 (tp30) REVERT: G 92 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7971 (mt-10) REVERT: H 65 ASP cc_start: 0.9320 (t70) cc_final: 0.9062 (t0) REVERT: H 80 TYR cc_start: 0.8403 (m-10) cc_final: 0.8098 (m-10) REVERT: K 51 THR cc_start: 0.9124 (p) cc_final: 0.8563 (t) REVERT: K 55 ILE cc_start: 0.7567 (mm) cc_final: 0.7239 (mm) REVERT: K 65 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6715 (mmm160) REVERT: K 93 GLN cc_start: 0.8521 (pp30) cc_final: 0.7959 (pp30) REVERT: K 109 PHE cc_start: 0.8876 (t80) cc_final: 0.8012 (t80) REVERT: K 113 GLN cc_start: 0.8287 (pm20) cc_final: 0.7734 (pm20) REVERT: K 257 TYR cc_start: 0.9513 (m-80) cc_final: 0.9276 (t80) REVERT: K 262 MET cc_start: 0.9215 (tpt) cc_final: 0.8805 (ttm) REVERT: K 265 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8279 (mm) REVERT: K 266 MET cc_start: 0.8720 (ttp) cc_final: 0.7993 (ttm) outliers start: 38 outliers final: 30 residues processed: 246 average time/residue: 0.1249 time to fit residues: 43.2212 Evaluate side-chains 246 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 265 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 121 optimal weight: 0.0010 chunk 81 optimal weight: 3.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.105213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065467 restraints weight = 44839.623| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.78 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14904 Z= 0.184 Angle : 0.652 27.295 21354 Z= 0.355 Chirality : 0.055 2.060 2431 Planarity : 0.005 0.115 1730 Dihedral : 29.281 169.445 4306 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.63 % Favored : 97.08 % Rotamer: Outliers : 4.15 % Allowed : 19.82 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.27), residues: 1028 helix: 2.50 (0.21), residues: 617 sheet: -1.22 (0.83), residues: 43 loop : -1.66 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.014 0.001 TYR G 39 PHE 0.012 0.002 PHE K 124 TRP 0.040 0.005 TRP K 276 HIS 0.006 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00419 (14899) covalent geometry : angle 0.64974 (21348) hydrogen bonds : bond 0.04098 ( 829) hydrogen bonds : angle 3.08887 ( 2098) metal coordination : bond 0.00909 ( 4) metal coordination : angle 3.26168 ( 6) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9070 (p) cc_final: 0.8794 (t) REVERT: B 93 GLN cc_start: 0.8570 (mp10) cc_final: 0.8135 (mp10) REVERT: C 90 ASP cc_start: 0.8505 (t70) cc_final: 0.7792 (t0) REVERT: C 91 GLU cc_start: 0.8482 (pm20) cc_final: 0.7712 (pm20) REVERT: C 92 GLU cc_start: 0.8539 (mp0) cc_final: 0.7264 (mp0) REVERT: E 45 THR cc_start: 0.8095 (t) cc_final: 0.7633 (p) REVERT: E 57 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.7754 (t) REVERT: E 59 GLU cc_start: 0.8165 (pm20) cc_final: 0.7939 (pm20) REVERT: E 94 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7806 (mm-30) REVERT: F 59 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8332 (tttt) REVERT: F 88 TYR cc_start: 0.8400 (m-10) cc_final: 0.7773 (m-10) REVERT: G 91 GLU cc_start: 0.8081 (tp30) cc_final: 0.7802 (tp30) REVERT: H 65 ASP cc_start: 0.8948 (t70) cc_final: 0.8653 (t0) REVERT: H 80 TYR cc_start: 0.8079 (m-10) cc_final: 0.7708 (m-10) REVERT: K 51 THR cc_start: 0.9013 (p) cc_final: 0.8397 (t) REVERT: K 55 ILE cc_start: 0.7476 (mm) cc_final: 0.7026 (mm) REVERT: K 71 TRP cc_start: 0.6002 (m-90) cc_final: 0.5074 (m100) REVERT: K 109 PHE cc_start: 0.8763 (t80) cc_final: 0.7883 (t80) REVERT: K 136 MET cc_start: 0.8427 (tpp) cc_final: 0.7882 (tmm) REVERT: K 188 TRP cc_start: 0.7371 (m100) cc_final: 0.6980 (m100) REVERT: K 196 ASP cc_start: 0.9318 (m-30) cc_final: 0.8392 (t0) REVERT: K 238 ILE cc_start: 0.7861 (pt) cc_final: 0.7167 (pt) REVERT: K 257 TYR cc_start: 0.9430 (OUTLIER) cc_final: 0.9191 (t80) outliers start: 36 outliers final: 25 residues processed: 258 average time/residue: 0.1253 time to fit residues: 45.6957 Evaluate side-chains 258 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.104091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064568 restraints weight = 45495.355| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.76 r_work: 0.2921 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 14904 Z= 0.201 Angle : 0.663 27.415 21354 Z= 0.358 Chirality : 0.055 2.052 2431 Planarity : 0.005 0.116 1730 Dihedral : 29.190 170.359 4306 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.92 % Favored : 96.79 % Rotamer: Outliers : 4.26 % Allowed : 20.62 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.27), residues: 1028 helix: 2.40 (0.21), residues: 617 sheet: -1.13 (0.84), residues: 43 loop : -1.65 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 76 TYR 0.019 0.002 TYR G 39 PHE 0.014 0.002 PHE A 67 TRP 0.030 0.004 TRP K 276 HIS 0.008 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00457 (14899) covalent geometry : angle 0.66060 (21348) hydrogen bonds : bond 0.04354 ( 829) hydrogen bonds : angle 3.11903 ( 2098) metal coordination : bond 0.00907 ( 4) metal coordination : angle 3.69476 ( 6) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9135 (mp) REVERT: B 30 THR cc_start: 0.9223 (p) cc_final: 0.8973 (t) REVERT: B 88 TYR cc_start: 0.9145 (m-10) cc_final: 0.7975 (m-10) REVERT: B 93 GLN cc_start: 0.8720 (mp10) cc_final: 0.8454 (mp10) REVERT: C 90 ASP cc_start: 0.8788 (t70) cc_final: 0.8118 (t0) REVERT: C 91 GLU cc_start: 0.8796 (pm20) cc_final: 0.8117 (pm20) REVERT: C 92 GLU cc_start: 0.8865 (mp0) cc_final: 0.7685 (mp0) REVERT: D 80 TYR cc_start: 0.8364 (m-10) cc_final: 0.8151 (m-80) REVERT: E 45 THR cc_start: 0.8131 (t) cc_final: 0.7670 (p) REVERT: E 57 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8034 (t) REVERT: E 59 GLU cc_start: 0.8693 (pm20) cc_final: 0.8430 (pm20) REVERT: E 94 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8469 (mm-30) REVERT: F 59 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8605 (tttt) REVERT: F 88 TYR cc_start: 0.8699 (m-10) cc_final: 0.8152 (m-10) REVERT: G 91 GLU cc_start: 0.8401 (tp30) cc_final: 0.8149 (tp30) REVERT: H 65 ASP cc_start: 0.9220 (t70) cc_final: 0.8942 (t0) REVERT: H 80 TYR cc_start: 0.8309 (m-10) cc_final: 0.7928 (m-10) REVERT: K 17 LYS cc_start: 0.2907 (pttt) cc_final: 0.1236 (pttp) REVERT: K 51 THR cc_start: 0.9024 (p) cc_final: 0.8559 (t) REVERT: K 55 ILE cc_start: 0.7362 (mm) cc_final: 0.6774 (mm) REVERT: K 71 TRP cc_start: 0.6272 (m-90) cc_final: 0.6007 (m100) REVERT: K 109 PHE cc_start: 0.8763 (t80) cc_final: 0.8180 (t80) REVERT: K 113 GLN cc_start: 0.7938 (pm20) cc_final: 0.7600 (pm20) REVERT: K 196 ASP cc_start: 0.9308 (m-30) cc_final: 0.8377 (t0) REVERT: K 257 TYR cc_start: 0.9499 (OUTLIER) cc_final: 0.9268 (t80) outliers start: 37 outliers final: 27 residues processed: 260 average time/residue: 0.1265 time to fit residues: 45.9895 Evaluate side-chains 258 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 93 GLN F 75 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.105913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067677 restraints weight = 44330.524| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.74 r_work: 0.2946 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 14904 Z= 0.147 Angle : 0.643 27.273 21354 Z= 0.347 Chirality : 0.054 2.057 2431 Planarity : 0.005 0.116 1730 Dihedral : 28.930 171.170 4306 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 3.46 % Allowed : 21.77 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.27), residues: 1028 helix: 2.64 (0.21), residues: 617 sheet: -0.59 (0.94), residues: 38 loop : -1.71 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.012 0.001 TYR G 39 PHE 0.019 0.001 PHE A 67 TRP 0.030 0.004 TRP K 188 HIS 0.004 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00327 (14899) covalent geometry : angle 0.64035 (21348) hydrogen bonds : bond 0.03813 ( 829) hydrogen bonds : angle 2.97034 ( 2098) metal coordination : bond 0.00738 ( 4) metal coordination : angle 3.33413 ( 6) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9114 (p) cc_final: 0.8856 (t) REVERT: B 88 TYR cc_start: 0.9064 (m-10) cc_final: 0.7886 (m-10) REVERT: C 90 ASP cc_start: 0.8679 (t70) cc_final: 0.8310 (t0) REVERT: C 91 GLU cc_start: 0.8807 (pm20) cc_final: 0.8229 (pm20) REVERT: C 92 GLU cc_start: 0.8884 (mp0) cc_final: 0.7925 (mp0) REVERT: D 29 THR cc_start: 0.6387 (m) cc_final: 0.6044 (t) REVERT: E 105 GLU cc_start: 0.8646 (tt0) cc_final: 0.8373 (mt-10) REVERT: F 59 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8452 (tttt) REVERT: F 88 TYR cc_start: 0.8651 (m-10) cc_final: 0.8130 (m-10) REVERT: G 36 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8807 (mmmm) REVERT: G 91 GLU cc_start: 0.8327 (tp30) cc_final: 0.8056 (tp30) REVERT: H 65 ASP cc_start: 0.9251 (t70) cc_final: 0.8974 (t0) REVERT: H 80 TYR cc_start: 0.8181 (m-10) cc_final: 0.7766 (m-10) REVERT: K 51 THR cc_start: 0.9019 (p) cc_final: 0.8546 (t) REVERT: K 55 ILE cc_start: 0.7081 (mm) cc_final: 0.6443 (mm) REVERT: K 65 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: K 100 GLN cc_start: 0.9392 (tp40) cc_final: 0.9069 (mm-40) REVERT: K 109 PHE cc_start: 0.8847 (t80) cc_final: 0.7991 (t80) REVERT: K 113 GLN cc_start: 0.7922 (pm20) cc_final: 0.7609 (pm20) REVERT: K 227 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9284 (mm) REVERT: K 257 TYR cc_start: 0.9485 (OUTLIER) cc_final: 0.9261 (t80) REVERT: K 262 MET cc_start: 0.9133 (tpt) cc_final: 0.8654 (ttm) REVERT: K 266 MET cc_start: 0.7934 (tpp) cc_final: 0.7621 (tpp) outliers start: 30 outliers final: 18 residues processed: 269 average time/residue: 0.1228 time to fit residues: 46.6979 Evaluate side-chains 251 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 276 TRP Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN E 76 GLN ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.104873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066004 restraints weight = 44765.167| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.75 r_work: 0.2892 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 14904 Z= 0.195 Angle : 0.665 27.412 21354 Z= 0.358 Chirality : 0.056 2.051 2431 Planarity : 0.005 0.117 1730 Dihedral : 29.006 171.272 4306 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 3.11 % Allowed : 23.04 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.27), residues: 1028 helix: 2.52 (0.21), residues: 617 sheet: -0.87 (0.85), residues: 43 loop : -1.65 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.023 0.002 TYR B 88 PHE 0.026 0.002 PHE K 64 TRP 0.027 0.004 TRP K 276 HIS 0.007 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00443 (14899) covalent geometry : angle 0.66272 (21348) hydrogen bonds : bond 0.04212 ( 829) hydrogen bonds : angle 3.11289 ( 2098) metal coordination : bond 0.01016 ( 4) metal coordination : angle 3.10320 ( 6) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9204 (p) cc_final: 0.8971 (t) REVERT: C 90 ASP cc_start: 0.8759 (t70) cc_final: 0.8402 (t0) REVERT: C 91 GLU cc_start: 0.8831 (pm20) cc_final: 0.8233 (pm20) REVERT: C 92 GLU cc_start: 0.8908 (mp0) cc_final: 0.7955 (mp0) REVERT: F 59 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8529 (tttt) REVERT: F 88 TYR cc_start: 0.8699 (m-10) cc_final: 0.8109 (m-10) REVERT: G 91 GLU cc_start: 0.8388 (tp30) cc_final: 0.8115 (tp30) REVERT: H 65 ASP cc_start: 0.9297 (t70) cc_final: 0.9020 (t0) REVERT: H 80 TYR cc_start: 0.8242 (m-10) cc_final: 0.7790 (m-10) REVERT: K 51 THR cc_start: 0.9051 (p) cc_final: 0.8607 (t) REVERT: K 55 ILE cc_start: 0.7182 (mm) cc_final: 0.6529 (mm) REVERT: K 100 GLN cc_start: 0.9374 (tp40) cc_final: 0.9040 (mm-40) REVERT: K 109 PHE cc_start: 0.8827 (t80) cc_final: 0.8038 (t80) REVERT: K 113 GLN cc_start: 0.7877 (pm20) cc_final: 0.7453 (pm20) REVERT: K 196 ASP cc_start: 0.9479 (m-30) cc_final: 0.8611 (t0) REVERT: K 227 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9274 (mm) REVERT: K 257 TYR cc_start: 0.9490 (m-80) cc_final: 0.9283 (t80) REVERT: K 262 MET cc_start: 0.9144 (tpt) cc_final: 0.8720 (ttm) REVERT: K 266 MET cc_start: 0.7856 (tpp) cc_final: 0.7595 (tpp) outliers start: 27 outliers final: 20 residues processed: 243 average time/residue: 0.1188 time to fit residues: 40.7934 Evaluate side-chains 242 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 276 TRP Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 110 optimal weight: 0.1980 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN D 79 HIS E 68 GLN ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.104798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065531 restraints weight = 44512.642| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.75 r_work: 0.2913 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 14904 Z= 0.175 Angle : 0.673 27.294 21354 Z= 0.361 Chirality : 0.055 2.057 2431 Planarity : 0.005 0.118 1730 Dihedral : 29.006 170.998 4306 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 2.76 % Allowed : 23.62 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.27), residues: 1028 helix: 2.56 (0.21), residues: 616 sheet: -0.90 (0.85), residues: 43 loop : -1.57 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 65 TYR 0.040 0.002 TYR B 88 PHE 0.033 0.002 PHE K 64 TRP 0.064 0.006 TRP K 35 HIS 0.008 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00396 (14899) covalent geometry : angle 0.67179 (21348) hydrogen bonds : bond 0.03972 ( 829) hydrogen bonds : angle 3.09564 ( 2098) metal coordination : bond 0.00861 ( 4) metal coordination : angle 2.86230 ( 6) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9192 (p) cc_final: 0.8973 (t) REVERT: B 44 LYS cc_start: 0.9272 (tttt) cc_final: 0.8969 (ttpt) REVERT: B 93 GLN cc_start: 0.8631 (mp10) cc_final: 0.8301 (mp10) REVERT: C 90 ASP cc_start: 0.8774 (t70) cc_final: 0.8449 (t0) REVERT: C 91 GLU cc_start: 0.8829 (pm20) cc_final: 0.8248 (pm20) REVERT: C 92 GLU cc_start: 0.8911 (mp0) cc_final: 0.7959 (mp0) REVERT: E 45 THR cc_start: 0.8161 (m) cc_final: 0.7926 (p) REVERT: F 59 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8548 (tttt) REVERT: F 88 TYR cc_start: 0.8676 (m-10) cc_final: 0.8129 (m-10) REVERT: G 36 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8776 (mmmm) REVERT: G 91 GLU cc_start: 0.8421 (tp30) cc_final: 0.8145 (tp30) REVERT: H 65 ASP cc_start: 0.9267 (t70) cc_final: 0.8993 (t0) REVERT: H 80 TYR cc_start: 0.8241 (m-10) cc_final: 0.7787 (m-10) REVERT: K 51 THR cc_start: 0.8999 (p) cc_final: 0.8672 (t) REVERT: K 100 GLN cc_start: 0.9361 (tp40) cc_final: 0.9019 (mm-40) REVERT: K 109 PHE cc_start: 0.8814 (t80) cc_final: 0.8085 (t80) REVERT: K 113 GLN cc_start: 0.7990 (pm20) cc_final: 0.7770 (pm20) REVERT: K 196 ASP cc_start: 0.9490 (m-30) cc_final: 0.8643 (t0) REVERT: K 227 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9255 (mm) REVERT: K 257 TYR cc_start: 0.9458 (OUTLIER) cc_final: 0.9249 (t80) REVERT: K 262 MET cc_start: 0.9142 (tpt) cc_final: 0.8727 (ttm) REVERT: K 266 MET cc_start: 0.7852 (tpp) cc_final: 0.7642 (tpp) outliers start: 24 outliers final: 21 residues processed: 247 average time/residue: 0.1248 time to fit residues: 43.6426 Evaluate side-chains 246 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 276 TRP Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.104888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066275 restraints weight = 45044.215| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.75 r_work: 0.2904 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14904 Z= 0.182 Angle : 0.680 27.348 21354 Z= 0.362 Chirality : 0.055 2.053 2431 Planarity : 0.005 0.117 1730 Dihedral : 28.988 171.200 4306 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.02 % Favored : 96.79 % Rotamer: Outliers : 2.88 % Allowed : 23.62 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.26), residues: 1028 helix: 2.53 (0.21), residues: 616 sheet: -0.92 (0.85), residues: 43 loop : -1.58 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 65 TYR 0.053 0.002 TYR B 88 PHE 0.034 0.002 PHE K 64 TRP 0.048 0.005 TRP K 35 HIS 0.007 0.001 HIS K 119 Details of bonding type rmsd covalent geometry : bond 0.00415 (14899) covalent geometry : angle 0.67805 (21348) hydrogen bonds : bond 0.04086 ( 829) hydrogen bonds : angle 3.11916 ( 2098) metal coordination : bond 0.00904 ( 4) metal coordination : angle 2.88293 ( 6) Misc. bond : bond 0.00109 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9206 (p) cc_final: 0.8979 (t) REVERT: B 44 LYS cc_start: 0.9301 (tttt) cc_final: 0.8959 (ttpt) REVERT: C 90 ASP cc_start: 0.8764 (t70) cc_final: 0.8410 (t0) REVERT: C 91 GLU cc_start: 0.8847 (pm20) cc_final: 0.8242 (pm20) REVERT: C 92 GLU cc_start: 0.8910 (mp0) cc_final: 0.7942 (mp0) REVERT: E 81 ASP cc_start: 0.9190 (t70) cc_final: 0.8876 (t70) REVERT: F 59 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8514 (tttt) REVERT: F 88 TYR cc_start: 0.8648 (m-10) cc_final: 0.8091 (m-10) REVERT: G 36 LYS cc_start: 0.9105 (mmtm) cc_final: 0.8804 (mmmm) REVERT: G 91 GLU cc_start: 0.8448 (tp30) cc_final: 0.8160 (tp30) REVERT: H 65 ASP cc_start: 0.9305 (t70) cc_final: 0.9024 (t0) REVERT: H 80 TYR cc_start: 0.8221 (m-10) cc_final: 0.7784 (m-10) REVERT: K 35 TRP cc_start: 0.9286 (t60) cc_final: 0.9061 (t60) REVERT: K 51 THR cc_start: 0.9106 (p) cc_final: 0.8829 (t) REVERT: K 100 GLN cc_start: 0.9350 (tp40) cc_final: 0.9085 (mm-40) REVERT: K 109 PHE cc_start: 0.8795 (t80) cc_final: 0.8075 (t80) REVERT: K 196 ASP cc_start: 0.9496 (m-30) cc_final: 0.8613 (t0) REVERT: K 227 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9256 (mm) REVERT: K 262 MET cc_start: 0.9165 (tpt) cc_final: 0.8780 (ttm) outliers start: 25 outliers final: 21 residues processed: 239 average time/residue: 0.1193 time to fit residues: 40.3383 Evaluate side-chains 245 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 119 HIS Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 276 TRP Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 27 GLN ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.102410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063147 restraints weight = 45122.549| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.77 r_work: 0.2844 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 14904 Z= 0.283 Angle : 0.722 27.463 21354 Z= 0.386 Chirality : 0.058 2.048 2431 Planarity : 0.005 0.117 1730 Dihedral : 29.229 170.067 4306 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.89 % Favored : 95.91 % Rotamer: Outliers : 3.23 % Allowed : 23.50 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.26), residues: 1028 helix: 2.28 (0.21), residues: 615 sheet: -0.86 (0.85), residues: 43 loop : -1.59 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 65 TYR 0.059 0.002 TYR B 88 PHE 0.034 0.002 PHE K 64 TRP 0.047 0.005 TRP K 35 HIS 0.005 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00648 (14899) covalent geometry : angle 0.72024 (21348) hydrogen bonds : bond 0.04959 ( 829) hydrogen bonds : angle 3.37270 ( 2098) metal coordination : bond 0.01409 ( 4) metal coordination : angle 3.05178 ( 6) Misc. bond : bond 0.00068 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.34 seconds wall clock time: 62 minutes 53.44 seconds (3773.44 seconds total)