Starting phenix.real_space_refine on Thu Jul 31 19:31:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eil_48086/07_2025/9eil_48086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eil_48086/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2025/9eil_48086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2025/9eil_48086.map" model { file = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2025/9eil_48086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2025/9eil_48086.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.13, per 1000 atoms: 0.65 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: 3.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.50 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: 5.87 Time building geometry restraints manager: 4.33 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: 3.000 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (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 TRP 0.006 0.001 TRP K 71 HIS 0.003 0.001 HIS K 133 PHE 0.009 0.001 PHE D 62 TYR 0.014 0.001 TYR K 5 ARG 0.002 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.10677 ( 829) hydrogen bonds : angle 3.89888 ( 2098) metal coordination : bond 0.01166 ( 4) metal coordination : angle 6.66086 ( 6) covalent geometry : bond 0.00446 (14899) covalent geometry : angle 0.66863 (21348) 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 : 1.173 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: 0.3814 time to fit residues: 188.0795 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 : 1.124 ------------------------------------------------------------------------------- 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 108 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 108 ASN F 25 ASN H 60 ASN H 106 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.104983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065224 restraints weight = 44543.768| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.85 r_work: 0.2880 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 14904 Z= 0.269 Angle : 0.709 27.440 21354 Z= 0.386 Chirality : 0.057 2.050 2431 Planarity : 0.006 0.104 1730 Dihedral : 29.223 170.715 4313 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Rotamer: Outliers : 5.76 % Allowed : 16.47 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1028 helix: 2.24 (0.21), residues: 618 sheet: -1.55 (0.89), residues: 36 loop : -1.58 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 276 HIS 0.010 0.002 HIS K 133 PHE 0.022 0.002 PHE K 124 TYR 0.021 0.002 TYR B 88 ARG 0.010 0.001 ARG K 264 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 829) hydrogen bonds : angle 3.30884 ( 2098) metal coordination : bond 0.01675 ( 4) metal coordination : angle 4.31083 ( 6) covalent geometry : bond 0.00612 (14899) covalent geometry : angle 0.70574 (21348) Misc. bond : bond 0.00057 ( 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 298 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 1.127 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: A 90 MET cc_start: 0.9196 (mmm) cc_final: 0.8934 (mmp) REVERT: B 74 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8890 (mm-30) REVERT: B 93 GLN cc_start: 0.8852 (mt0) cc_final: 0.8603 (mp10) REVERT: C 90 ASP cc_start: 0.8689 (t70) cc_final: 0.8228 (t70) REVERT: C 91 GLU cc_start: 0.8658 (pm20) cc_final: 0.8229 (pm20) REVERT: C 92 GLU cc_start: 0.8746 (mp0) cc_final: 0.7801 (mp0) REVERT: E 45 THR cc_start: 0.8049 (t) cc_final: 0.7707 (p) REVERT: E 60 LEU cc_start: 0.9365 (mt) cc_final: 0.9069 (mt) REVERT: E 94 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8399 (mm-30) REVERT: E 105 GLU cc_start: 0.8816 (tt0) cc_final: 0.8424 (mt-10) REVERT: F 59 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8586 (tttt) REVERT: F 88 TYR cc_start: 0.8604 (m-10) cc_final: 0.8178 (m-10) REVERT: G 91 GLU cc_start: 0.8483 (tp30) cc_final: 0.8256 (tp30) REVERT: G 92 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7481 (mt-10) REVERT: H 65 ASP cc_start: 0.9204 (t70) cc_final: 0.8990 (t0) REVERT: H 73 GLU cc_start: 0.8828 (tp30) cc_final: 0.8551 (tp30) REVERT: H 80 TYR cc_start: 0.8354 (m-10) cc_final: 0.7748 (m-10) REVERT: H 90 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7501 (mm-30) REVERT: K 51 THR cc_start: 0.8971 (p) cc_final: 0.8487 (t) REVERT: K 93 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8899 (tp40) REVERT: K 109 PHE cc_start: 0.8814 (t80) cc_final: 0.7884 (t80) REVERT: K 113 GLN cc_start: 0.8164 (pm20) cc_final: 0.7662 (pm20) REVERT: K 131 GLU cc_start: 0.9159 (mp0) cc_final: 0.8804 (pm20) REVERT: K 147 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7733 (tm-30) REVERT: K 196 ASP cc_start: 0.9215 (m-30) cc_final: 0.8368 (t0) REVERT: K 257 TYR cc_start: 0.9493 (m-80) cc_final: 0.9261 (t80) REVERT: K 265 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8562 (mm) REVERT: K 266 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8341 (ptm) outliers start: 50 outliers final: 26 residues processed: 280 average time/residue: 0.3041 time to fit residues: 116.7433 Evaluate side-chains 253 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 B residue 50 ILE Chi-restraints excluded: chain B residue 80 THR 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 87 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 33 SER 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 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 212 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 266 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 27 GLN B 93 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN K 95 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.106749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067349 restraints weight = 44543.090| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.78 r_work: 0.2945 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3113 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= 0.169 Angle : 0.659 27.256 21354 Z= 0.355 Chirality : 0.055 2.060 2431 Planarity : 0.005 0.109 1730 Dihedral : 29.157 170.023 4309 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.92 % Favored : 96.79 % Rotamer: Outliers : 3.69 % Allowed : 18.09 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1028 helix: 2.51 (0.21), residues: 618 sheet: -1.32 (0.91), residues: 36 loop : -1.52 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP K 276 HIS 0.004 0.001 HIS K 68 PHE 0.010 0.001 PHE K 64 TYR 0.010 0.001 TYR G 39 ARG 0.011 0.001 ARG K 205 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 829) hydrogen bonds : angle 3.11176 ( 2098) metal coordination : bond 0.01073 ( 4) metal coordination : angle 4.12865 ( 6) covalent geometry : bond 0.00383 (14899) covalent geometry : angle 0.65520 (21348) Misc. bond : bond 0.00028 ( 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: 32 poor density : 260 time to evaluate : 1.139 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: A 90 MET cc_start: 0.9199 (mmm) cc_final: 0.8879 (mmp) REVERT: A 133 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 74 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8787 (mm-30) REVERT: B 88 TYR cc_start: 0.9095 (m-10) cc_final: 0.7951 (m-10) REVERT: C 90 ASP cc_start: 0.8671 (t70) cc_final: 0.8126 (t0) REVERT: C 91 GLU cc_start: 0.8670 (pm20) cc_final: 0.8067 (pm20) REVERT: C 92 GLU cc_start: 0.8776 (mp0) cc_final: 0.7719 (mp0) REVERT: E 45 THR cc_start: 0.8104 (t) cc_final: 0.7745 (p) REVERT: E 54 TYR cc_start: 0.8965 (m-80) cc_final: 0.8724 (m-80) REVERT: E 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8049 (pm20) REVERT: E 105 GLU cc_start: 0.8781 (tt0) cc_final: 0.8381 (mt-10) REVERT: F 59 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8516 (tttt) REVERT: F 88 TYR cc_start: 0.8583 (m-10) cc_final: 0.8060 (m-10) REVERT: G 91 GLU cc_start: 0.8353 (tp30) cc_final: 0.8045 (tp30) REVERT: H 65 ASP cc_start: 0.9147 (t70) cc_final: 0.8895 (t0) REVERT: H 80 TYR cc_start: 0.8289 (m-10) cc_final: 0.7734 (m-10) REVERT: H 90 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7477 (mm-30) REVERT: K 17 LYS cc_start: 0.3890 (pttm) cc_final: 0.0746 (tppt) REVERT: K 71 TRP cc_start: 0.6414 (m100) cc_final: 0.5935 (m100) REVERT: K 109 PHE cc_start: 0.8871 (t80) cc_final: 0.8180 (t80) REVERT: K 113 GLN cc_start: 0.8041 (pm20) cc_final: 0.7657 (pm20) REVERT: K 145 LYS cc_start: 0.9356 (tmmt) cc_final: 0.9146 (ttpp) REVERT: K 147 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7737 (tm-30) REVERT: K 196 ASP cc_start: 0.9341 (m-30) cc_final: 0.8437 (t0) REVERT: K 257 TYR cc_start: 0.9480 (m-80) cc_final: 0.9226 (t80) outliers start: 32 outliers final: 26 residues processed: 275 average time/residue: 0.3138 time to fit residues: 117.4676 Evaluate side-chains 260 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 104 GLN 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 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 213 LEU Chi-restraints excluded: chain K residue 236 LEU 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 89 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 102 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 60 ASN 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 = 0.4049 r_free = 0.4049 target = 0.107054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067450 restraints weight = 44054.272| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.77 r_work: 0.2953 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3460 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= 0.160 Angle : 0.645 27.388 21354 Z= 0.350 Chirality : 0.055 2.054 2431 Planarity : 0.005 0.113 1730 Dihedral : 29.013 171.037 4306 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Rotamer: Outliers : 3.92 % Allowed : 19.59 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1028 helix: 2.61 (0.21), residues: 619 sheet: -0.91 (0.93), residues: 36 loop : -1.52 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 188 HIS 0.005 0.001 HIS K 133 PHE 0.009 0.001 PHE E 67 TYR 0.017 0.001 TYR D 80 ARG 0.008 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 829) hydrogen bonds : angle 3.05888 ( 2098) metal coordination : bond 0.01001 ( 4) metal coordination : angle 3.80243 ( 6) covalent geometry : bond 0.00359 (14899) covalent geometry : angle 0.64235 (21348) Misc. bond : bond 0.00070 ( 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 285 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 1.090 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 133 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 74 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8767 (mm-30) REVERT: B 93 GLN cc_start: 0.8817 (mp10) cc_final: 0.8416 (mp10) REVERT: C 90 ASP cc_start: 0.8682 (t70) cc_final: 0.8099 (t0) REVERT: C 91 GLU cc_start: 0.8725 (pm20) cc_final: 0.8102 (pm20) REVERT: C 92 GLU cc_start: 0.8789 (mp0) cc_final: 0.7662 (mp0) REVERT: E 45 THR cc_start: 0.8041 (t) cc_final: 0.7590 (p) REVERT: E 56 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8677 (ptpt) REVERT: E 59 GLU cc_start: 0.8598 (pm20) cc_final: 0.8372 (pm20) REVERT: E 105 GLU cc_start: 0.8764 (tt0) cc_final: 0.8347 (mt-10) REVERT: F 59 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8524 (tttt) REVERT: F 88 TYR cc_start: 0.8581 (m-10) cc_final: 0.8056 (m-10) REVERT: G 38 ASN cc_start: 0.8309 (m-40) cc_final: 0.8067 (m-40) REVERT: G 91 GLU cc_start: 0.8288 (tp30) cc_final: 0.8029 (tp30) REVERT: H 65 ASP cc_start: 0.9152 (t70) cc_final: 0.8886 (t0) REVERT: H 80 TYR cc_start: 0.8252 (m-10) cc_final: 0.7732 (m-10) REVERT: K 17 LYS cc_start: 0.3976 (pttm) cc_final: 0.1011 (tptt) REVERT: K 109 PHE cc_start: 0.8959 (t80) cc_final: 0.8360 (t80) REVERT: K 113 GLN cc_start: 0.8245 (pm20) cc_final: 0.7282 (pp30) REVERT: K 136 MET cc_start: 0.8317 (tpp) cc_final: 0.7859 (tmm) REVERT: K 145 LYS cc_start: 0.9365 (tmmt) cc_final: 0.9137 (tmmt) REVERT: K 196 ASP cc_start: 0.9329 (m-30) cc_final: 0.8455 (t0) REVERT: K 245 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8623 (mmmt) REVERT: K 257 TYR cc_start: 0.9488 (m-80) cc_final: 0.9244 (t80) outliers start: 34 outliers final: 25 residues processed: 270 average time/residue: 0.2994 time to fit residues: 110.8520 Evaluate side-chains 264 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 E residue 56 LYS 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 84 MET 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 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 120 VAL Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 93 GLN H 60 ASN K 100 GLN K 119 HIS ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.105788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066258 restraints weight = 44817.690| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.76 r_work: 0.2929 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3732 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= 0.187 Angle : 0.653 27.393 21354 Z= 0.353 Chirality : 0.055 2.056 2431 Planarity : 0.005 0.115 1730 Dihedral : 29.029 171.035 4306 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.72 % Favored : 96.98 % Rotamer: Outliers : 3.92 % Allowed : 20.39 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 1028 helix: 2.57 (0.21), residues: 618 sheet: -0.78 (0.95), residues: 36 loop : -1.58 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP K 188 HIS 0.013 0.001 HIS K 246 PHE 0.012 0.001 PHE A 67 TYR 0.021 0.002 TYR E 54 ARG 0.012 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 829) hydrogen bonds : angle 3.07417 ( 2098) metal coordination : bond 0.01108 ( 4) metal coordination : angle 3.57132 ( 6) covalent geometry : bond 0.00424 (14899) covalent geometry : angle 0.65015 (21348) Misc. bond : bond 0.00092 ( 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 279 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.240 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: B 30 THR cc_start: 0.9154 (p) cc_final: 0.8904 (t) REVERT: B 74 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8758 (mm-30) REVERT: B 93 GLN cc_start: 0.8703 (mp10) cc_final: 0.8429 (mp10) REVERT: C 90 ASP cc_start: 0.8702 (t70) cc_final: 0.8027 (t0) REVERT: C 91 GLU cc_start: 0.8745 (pm20) cc_final: 0.8079 (pm20) REVERT: C 92 GLU cc_start: 0.8811 (mp0) cc_final: 0.7640 (mp0) REVERT: D 29 THR cc_start: 0.6350 (m) cc_final: 0.6083 (t) REVERT: E 45 THR cc_start: 0.8062 (t) cc_final: 0.7802 (p) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.8404 (pm20) REVERT: E 105 GLU cc_start: 0.8782 (tt0) cc_final: 0.8331 (mt-10) REVERT: F 59 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8548 (tttt) REVERT: F 88 TYR cc_start: 0.8669 (m-10) cc_final: 0.8072 (m-10) REVERT: G 91 GLU cc_start: 0.8322 (tp30) cc_final: 0.8070 (tp30) REVERT: H 65 ASP cc_start: 0.9216 (t70) cc_final: 0.8939 (t0) REVERT: H 80 TYR cc_start: 0.8276 (m-10) cc_final: 0.7742 (m-10) REVERT: K 17 LYS cc_start: 0.3735 (pttm) cc_final: 0.1058 (tptt) REVERT: K 109 PHE cc_start: 0.9016 (t80) cc_final: 0.8242 (t80) REVERT: K 113 GLN cc_start: 0.8210 (pm20) cc_final: 0.7340 (pp30) REVERT: K 196 ASP cc_start: 0.9350 (m-30) cc_final: 0.8517 (t0) REVERT: K 257 TYR cc_start: 0.9487 (m-80) cc_final: 0.9251 (t80) REVERT: K 262 MET cc_start: 0.8137 (ttp) cc_final: 0.7860 (ttp) outliers start: 34 outliers final: 25 residues processed: 264 average time/residue: 0.3066 time to fit residues: 111.4729 Evaluate side-chains 258 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 84 MET 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 103 LEU Chi-restraints excluded: chain K residue 10 SER 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 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN H 60 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.105930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067370 restraints weight = 44270.592| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.75 r_work: 0.2946 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3948 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= 0.159 Angle : 0.660 27.326 21354 Z= 0.353 Chirality : 0.055 2.059 2431 Planarity : 0.005 0.117 1730 Dihedral : 28.916 171.347 4306 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.43 % Favored : 97.28 % Rotamer: Outliers : 3.34 % Allowed : 21.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1028 helix: 2.69 (0.21), residues: 617 sheet: -1.06 (0.85), residues: 44 loop : -1.53 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP K 276 HIS 0.016 0.001 HIS K 246 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR G 57 ARG 0.010 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 829) hydrogen bonds : angle 3.00272 ( 2098) metal coordination : bond 0.00968 ( 4) metal coordination : angle 3.84875 ( 6) covalent geometry : bond 0.00358 (14899) covalent geometry : angle 0.65728 (21348) Misc. bond : bond 0.00093 ( 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 279 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 1.127 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: 0.9133 (p) cc_final: 0.8875 (t) REVERT: B 74 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8787 (mm-30) REVERT: B 88 TYR cc_start: 0.9025 (m-10) cc_final: 0.8775 (m-10) REVERT: B 93 GLN cc_start: 0.8680 (mp10) cc_final: 0.8474 (mp10) REVERT: C 90 ASP cc_start: 0.8694 (t70) cc_final: 0.8092 (t70) REVERT: C 91 GLU cc_start: 0.8752 (pm20) cc_final: 0.8087 (pm20) REVERT: C 92 GLU cc_start: 0.8832 (mp0) cc_final: 0.7755 (mp0) REVERT: D 29 THR cc_start: 0.6385 (m) cc_final: 0.6114 (t) REVERT: E 45 THR cc_start: 0.8014 (t) cc_final: 0.7502 (p) REVERT: E 59 GLU cc_start: 0.8647 (pm20) cc_final: 0.8415 (pm20) REVERT: E 105 GLU cc_start: 0.8770 (tt0) cc_final: 0.8437 (mt-10) REVERT: F 59 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8505 (tttt) REVERT: F 88 TYR cc_start: 0.8660 (m-10) cc_final: 0.8108 (m-10) REVERT: G 36 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8836 (mmmm) REVERT: G 91 GLU cc_start: 0.8245 (tp30) cc_final: 0.8006 (tp30) REVERT: H 65 ASP cc_start: 0.9222 (t70) cc_final: 0.8943 (t0) REVERT: H 80 TYR cc_start: 0.8237 (m-10) cc_final: 0.7749 (m-10) REVERT: K 17 LYS cc_start: 0.3820 (pttm) cc_final: 0.1054 (tppt) REVERT: K 109 PHE cc_start: 0.9049 (t80) cc_final: 0.8193 (t80) REVERT: K 113 GLN cc_start: 0.8215 (pm20) cc_final: 0.7308 (pp30) REVERT: K 196 ASP cc_start: 0.9339 (m-30) cc_final: 0.8498 (t0) REVERT: K 257 TYR cc_start: 0.9479 (m-80) cc_final: 0.9277 (t80) outliers start: 29 outliers final: 24 residues processed: 264 average time/residue: 0.3060 time to fit residues: 111.0280 Evaluate side-chains 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 GLN 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 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 276 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 93 GLN H 60 ASN K 119 HIS ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.102150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062680 restraints weight = 45170.588| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.78 r_work: 0.2818 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 14904 Z= 0.349 Angle : 0.751 27.488 21354 Z= 0.402 Chirality : 0.059 2.055 2431 Planarity : 0.006 0.120 1730 Dihedral : 29.374 169.459 4306 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.01 % Rotamer: Outliers : 4.72 % Allowed : 20.39 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1028 helix: 2.12 (0.21), residues: 617 sheet: -1.02 (0.82), residues: 43 loop : -1.65 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP K 276 HIS 0.009 0.002 HIS K 255 PHE 0.023 0.002 PHE A 67 TYR 0.017 0.002 TYR G 57 ARG 0.009 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 829) hydrogen bonds : angle 3.47096 ( 2098) metal coordination : bond 0.02098 ( 4) metal coordination : angle 4.03050 ( 6) covalent geometry : bond 0.00796 (14899) covalent geometry : angle 0.74847 (21348) Misc. bond : bond 0.00073 ( 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 254 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.120 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 44 LYS cc_start: 0.9310 (tttt) cc_final: 0.8998 (ttpt) REVERT: B 74 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8824 (mm-30) REVERT: B 88 TYR cc_start: 0.9086 (m-10) cc_final: 0.8714 (m-10) REVERT: C 90 ASP cc_start: 0.8773 (t70) cc_final: 0.8521 (t70) REVERT: C 91 GLU cc_start: 0.8798 (pm20) cc_final: 0.8235 (pm20) REVERT: C 92 GLU cc_start: 0.8900 (mp0) cc_final: 0.8063 (mp0) REVERT: D 29 THR cc_start: 0.6739 (m) cc_final: 0.6383 (t) REVERT: E 45 THR cc_start: 0.8172 (t) cc_final: 0.7909 (p) REVERT: E 59 GLU cc_start: 0.8623 (pm20) cc_final: 0.8391 (pm20) REVERT: E 94 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8469 (mm-30) REVERT: F 59 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8667 (tttt) REVERT: F 88 TYR cc_start: 0.8889 (m-10) cc_final: 0.8257 (m-10) REVERT: G 91 GLU cc_start: 0.8586 (tp30) cc_final: 0.8286 (tp30) REVERT: H 65 ASP cc_start: 0.9321 (t70) cc_final: 0.9051 (t0) REVERT: H 80 TYR cc_start: 0.8327 (m-10) cc_final: 0.8011 (m-10) REVERT: K 109 PHE cc_start: 0.9060 (t80) cc_final: 0.8222 (t80) REVERT: K 113 GLN cc_start: 0.8344 (pm20) cc_final: 0.8092 (pm20) REVERT: K 196 ASP cc_start: 0.9378 (m-30) cc_final: 0.8415 (t0) outliers start: 41 outliers final: 30 residues processed: 242 average time/residue: 0.2984 time to fit residues: 100.8232 Evaluate side-chains 242 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 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 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 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 51 THR Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 276 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 93 GLN K 119 HIS K 147 GLN K 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.104582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065122 restraints weight = 44866.384| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.75 r_work: 0.2939 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14904 Z= 0.160 Angle : 0.671 27.173 21354 Z= 0.358 Chirality : 0.055 2.068 2431 Planarity : 0.005 0.120 1730 Dihedral : 29.148 169.533 4306 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 3.11 % Allowed : 22.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.27), residues: 1028 helix: 2.47 (0.21), residues: 617 sheet: -0.94 (0.84), residues: 43 loop : -1.63 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP K 276 HIS 0.005 0.001 HIS K 95 PHE 0.019 0.001 PHE K 124 TYR 0.015 0.001 TYR E 54 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 829) hydrogen bonds : angle 3.12096 ( 2098) metal coordination : bond 0.00947 ( 4) metal coordination : angle 3.42794 ( 6) covalent geometry : bond 0.00358 (14899) covalent geometry : angle 0.66910 (21348) Misc. bond : bond 0.00101 ( 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 264 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.140 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: 0.9192 (p) cc_final: 0.8956 (t) REVERT: B 74 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8741 (mm-30) REVERT: B 88 TYR cc_start: 0.9065 (m-10) cc_final: 0.8812 (m-10) REVERT: B 93 GLN cc_start: 0.8785 (mp10) cc_final: 0.8540 (mp10) REVERT: C 90 ASP cc_start: 0.8739 (t70) cc_final: 0.8482 (t70) REVERT: C 91 GLU cc_start: 0.8804 (pm20) cc_final: 0.8185 (pm20) REVERT: C 92 GLU cc_start: 0.8873 (mp0) cc_final: 0.8021 (mp0) REVERT: E 45 THR cc_start: 0.8126 (t) cc_final: 0.7657 (p) REVERT: E 59 GLU cc_start: 0.8708 (pm20) cc_final: 0.8473 (pm20) REVERT: E 60 LEU cc_start: 0.9309 (mt) cc_final: 0.9089 (mt) REVERT: E 94 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8439 (mm-30) REVERT: F 59 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8547 (tttt) REVERT: F 88 TYR cc_start: 0.8768 (m-10) cc_final: 0.8243 (m-10) REVERT: G 91 GLU cc_start: 0.8422 (tp30) cc_final: 0.8151 (tp30) REVERT: H 65 ASP cc_start: 0.9255 (t70) cc_final: 0.8974 (t0) REVERT: H 80 TYR cc_start: 0.8247 (m-10) cc_final: 0.7894 (m-10) REVERT: K 109 PHE cc_start: 0.8964 (t80) cc_final: 0.8079 (t80) REVERT: K 113 GLN cc_start: 0.8229 (pm20) cc_final: 0.7816 (pm20) REVERT: K 196 ASP cc_start: 0.9339 (m-30) cc_final: 0.8393 (t0) REVERT: K 227 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9296 (mm) REVERT: K 257 TYR cc_start: 0.9344 (t80) cc_final: 0.8931 (t80) outliers start: 27 outliers final: 22 residues processed: 250 average time/residue: 0.3078 time to fit residues: 107.0597 Evaluate side-chains 248 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 86 SER 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 G residue 78 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 99 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 194 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 81 ASN K 43 GLN K 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.105794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066453 restraints weight = 45291.754| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.76 r_work: 0.2976 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 14904 Z= 0.161 Angle : 0.666 27.382 21354 Z= 0.355 Chirality : 0.055 2.050 2431 Planarity : 0.005 0.120 1730 Dihedral : 28.913 171.422 4306 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 3.00 % Allowed : 22.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1028 helix: 2.57 (0.21), residues: 618 sheet: -0.84 (0.86), residues: 43 loop : -1.53 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP K 276 HIS 0.006 0.001 HIS K 95 PHE 0.017 0.001 PHE A 67 TYR 0.014 0.001 TYR G 57 ARG 0.008 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 829) hydrogen bonds : angle 3.07306 ( 2098) metal coordination : bond 0.00896 ( 4) metal coordination : angle 3.23221 ( 6) covalent geometry : bond 0.00365 (14899) covalent geometry : angle 0.66380 (21348) Misc. bond : bond 0.00088 ( 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 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8703 (ptmt) REVERT: A 125 GLN cc_start: 0.9297 (mt0) cc_final: 0.8881 (mt0) REVERT: B 74 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8722 (mm-30) REVERT: B 88 TYR cc_start: 0.9041 (m-10) cc_final: 0.8804 (m-10) REVERT: B 93 GLN cc_start: 0.8751 (mp10) cc_final: 0.8524 (mp10) REVERT: C 90 ASP cc_start: 0.8760 (t70) cc_final: 0.8436 (t0) REVERT: C 91 GLU cc_start: 0.8819 (pm20) cc_final: 0.8258 (pm20) REVERT: C 92 GLU cc_start: 0.8896 (mp0) cc_final: 0.7986 (mp0) REVERT: E 45 THR cc_start: 0.8175 (t) cc_final: 0.7880 (p) REVERT: E 59 GLU cc_start: 0.8683 (pm20) cc_final: 0.8460 (pm20) REVERT: E 60 LEU cc_start: 0.9334 (mt) cc_final: 0.9085 (mt) REVERT: F 59 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8545 (tttt) REVERT: F 88 TYR cc_start: 0.8689 (m-10) cc_final: 0.8024 (m-10) REVERT: G 91 GLU cc_start: 0.8391 (tp30) cc_final: 0.8137 (tp30) REVERT: H 65 ASP cc_start: 0.9209 (t70) cc_final: 0.8941 (t0) REVERT: H 80 TYR cc_start: 0.8213 (m-10) cc_final: 0.7705 (m-10) REVERT: K 65 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7776 (mmt-90) REVERT: K 109 PHE cc_start: 0.8836 (t80) cc_final: 0.8022 (t80) REVERT: K 131 GLU cc_start: 0.8955 (pm20) cc_final: 0.8646 (pm20) REVERT: K 196 ASP cc_start: 0.9350 (m-30) cc_final: 0.8392 (t0) REVERT: K 227 LEU cc_start: 0.9600 (tt) cc_final: 0.9276 (mm) REVERT: K 257 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8906 (t80) REVERT: K 264 ARG cc_start: 0.8956 (tpt170) cc_final: 0.8526 (mmm-85) outliers start: 26 outliers final: 19 residues processed: 246 average time/residue: 0.2960 time to fit residues: 101.4150 Evaluate side-chains 243 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 86 SER 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 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 194 ASP 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 122 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 57 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.105851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066759 restraints weight = 44931.571| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.75 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14904 Z= 0.157 Angle : 0.678 27.322 21354 Z= 0.360 Chirality : 0.055 2.054 2431 Planarity : 0.005 0.121 1730 Dihedral : 28.849 171.379 4306 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 2.53 % Allowed : 23.27 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1028 helix: 2.57 (0.21), residues: 618 sheet: -0.78 (0.88), residues: 43 loop : -1.51 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP K 276 HIS 0.004 0.001 HIS K 268 PHE 0.014 0.001 PHE K 124 TYR 0.016 0.001 TYR G 57 ARG 0.009 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 829) hydrogen bonds : angle 3.17730 ( 2098) metal coordination : bond 0.00819 ( 4) metal coordination : angle 3.05050 ( 6) covalent geometry : bond 0.00354 (14899) covalent geometry : angle 0.67609 (21348) Misc. bond : bond 0.00083 ( 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 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 1.122 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 122 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8524 (ptmt) REVERT: A 125 GLN cc_start: 0.9072 (mt0) cc_final: 0.8579 (mt0) REVERT: B 74 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8126 (mm-30) REVERT: B 88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8453 (m-10) REVERT: B 93 GLN cc_start: 0.8601 (mp10) cc_final: 0.8345 (mp10) REVERT: C 90 ASP cc_start: 0.8460 (t70) cc_final: 0.8078 (t0) REVERT: C 91 GLU cc_start: 0.8514 (pm20) cc_final: 0.7850 (pm20) REVERT: C 92 GLU cc_start: 0.8580 (mp0) cc_final: 0.7531 (mp0) REVERT: E 60 LEU cc_start: 0.9291 (mt) cc_final: 0.9028 (mt) REVERT: F 59 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8309 (tttt) REVERT: F 88 TYR cc_start: 0.8392 (m-10) cc_final: 0.7732 (m-10) REVERT: G 91 GLU cc_start: 0.8065 (tp30) cc_final: 0.7825 (tp30) REVERT: H 65 ASP cc_start: 0.8924 (t70) cc_final: 0.8627 (t0) REVERT: H 80 TYR cc_start: 0.7955 (m-10) cc_final: 0.7538 (m-10) REVERT: K 109 PHE cc_start: 0.8815 (t80) cc_final: 0.7935 (t80) REVERT: K 114 ASN cc_start: 0.8728 (p0) cc_final: 0.8454 (p0) REVERT: K 131 GLU cc_start: 0.8786 (pm20) cc_final: 0.8410 (pm20) REVERT: K 196 ASP cc_start: 0.9378 (m-30) cc_final: 0.8410 (t0) REVERT: K 227 LEU cc_start: 0.9598 (tt) cc_final: 0.9289 (mm) REVERT: K 264 ARG cc_start: 0.8938 (tpt170) cc_final: 0.8549 (mmm-85) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.2977 time to fit residues: 101.8862 Evaluate side-chains 243 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 86 SER 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 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 276 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.0170 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067039 restraints weight = 45279.290| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.74 r_work: 0.2993 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14904 Z= 0.153 Angle : 0.690 27.311 21354 Z= 0.364 Chirality : 0.055 2.054 2431 Planarity : 0.005 0.121 1730 Dihedral : 28.766 171.875 4306 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 2.30 % Allowed : 23.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.27), residues: 1028 helix: 2.58 (0.21), residues: 619 sheet: -0.79 (0.88), residues: 43 loop : -1.43 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP K 35 HIS 0.004 0.001 HIS K 133 PHE 0.013 0.001 PHE K 124 TYR 0.014 0.001 TYR G 57 ARG 0.007 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 829) hydrogen bonds : angle 3.14559 ( 2098) metal coordination : bond 0.00764 ( 4) metal coordination : angle 3.02742 ( 6) covalent geometry : bond 0.00343 (14899) covalent geometry : angle 0.68841 (21348) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8163.94 seconds wall clock time: 140 minutes 53.10 seconds (8453.10 seconds total)