Starting phenix.real_space_refine on Thu Aug 6 17:52:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uw1_42636/08_2026/8uw1_42636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uw1_42636/08_2026/8uw1_42636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uw1_42636/08_2026/8uw1_42636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uw1_42636/08_2026/8uw1_42636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uw1_42636/08_2026/8uw1_42636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uw1_42636/08_2026/8uw1_42636.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5964 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 13 5.16 5 C 6726 2.51 5 N 2282 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12164 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 745 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 29} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 2.26, per 1000 atoms: 0.19 Number of scatterers: 12164 At special positions: 0 Unit cell: (84.15, 120.7, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 292 15.00 O 2851 8.00 N 2282 7.00 C 6726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 244.5 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 68.7% alpha, 3.1% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.594A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.592A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.588A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.667A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.618A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.592A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.517A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.790A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.627A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.690A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.770A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.625A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.722A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 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 120 removed outlier: 3.540A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG A 83 " --> pdb=" O VAL B 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.308A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.821A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.300A 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 'G' and resid 77 through 78 394 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2103 1.33 - 1.45: 4333 1.45 - 1.57: 5929 1.57 - 1.69: 582 1.69 - 1.81: 24 Bond restraints: 12971 Sorted by residual: bond pdb=" C3' DG J 70 " pdb=" O3' DG J 70 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C3' DG I 122 " pdb=" O3' DG I 122 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C3' DC I 123 " pdb=" O3' DC I 123 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.12e+00 ... (remaining 12966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 17816 1.94 - 3.88: 912 3.88 - 5.82: 37 5.82 - 7.77: 3 7.77 - 9.71: 3 Bond angle restraints: 18771 Sorted by residual: angle pdb=" C3' DA J 73 " pdb=" O3' DA J 73 " pdb=" P DA J 74 " ideal model delta sigma weight residual 119.70 109.99 9.71 1.20e+00 6.94e-01 6.55e+01 angle pdb=" C3' DG J 72 " pdb=" O3' DG J 72 " pdb=" P DA J 73 " ideal model delta sigma weight residual 119.70 110.32 9.38 1.20e+00 6.94e-01 6.11e+01 angle pdb=" C3' DA J 71 " pdb=" O3' DA J 71 " pdb=" P DG J 72 " ideal model delta sigma weight residual 119.70 110.39 9.31 1.20e+00 6.94e-01 6.02e+01 angle pdb=" C3' DT J 75 " pdb=" O3' DT J 75 " pdb=" P DC J 76 " ideal model delta sigma weight residual 119.70 112.76 6.94 1.20e+00 6.94e-01 3.35e+01 angle pdb=" C3' DA J 74 " pdb=" O3' DA J 74 " pdb=" P DT J 75 " ideal model delta sigma weight residual 119.70 113.36 6.34 1.20e+00 6.94e-01 2.79e+01 ... (remaining 18766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 5685 35.79 - 71.58: 1359 71.58 - 107.36: 12 107.36 - 143.15: 0 143.15 - 178.94: 2 Dihedral angle restraints: 7058 sinusoidal: 4799 harmonic: 2259 Sorted by residual: dihedral pdb=" C4' DA J 110 " pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " pdb=" P DC J 111 " ideal model delta sinusoidal sigma weight residual -140.00 38.94 -178.94 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 42.87 177.13 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1977 0.093 - 0.187: 150 0.187 - 0.280: 3 0.280 - 0.373: 0 0.373 - 0.466: 6 Chirality restraints: 2136 Sorted by residual: chirality pdb=" P DA J 71 " pdb=" OP1 DA J 71 " pdb=" OP2 DA J 71 " pdb=" O5' DA J 71 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" P DT J 75 " pdb=" OP1 DT J 75 " pdb=" OP2 DT J 75 " pdb=" O5' DT J 75 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" P DG J 72 " pdb=" OP1 DG J 72 " pdb=" OP2 DG J 72 " pdb=" O5' DG J 72 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 2133 not shown) Planarity restraints: 1370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 141 " -0.024 2.00e-02 2.50e+03 1.12e-02 3.46e+00 pdb=" N9 DA I 141 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 141 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 141 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 141 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 141 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA I 141 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA I 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 131 " -0.026 2.00e-02 2.50e+03 1.10e-02 3.35e+00 pdb=" N9 DA I 131 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 131 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 131 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 131 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 131 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 131 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 131 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.17e+00 pdb=" N9 DA I 39 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.002 2.00e-02 2.50e+03 ... (remaining 1367 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2462 2.80 - 3.32: 9769 3.32 - 3.85: 22246 3.85 - 4.37: 27730 4.37 - 4.90: 38817 Nonbonded interactions: 101024 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.273 3.120 nonbonded pdb=" OE1 GLN E 125 " pdb=" NH1 ARG E 134 " model vdw 2.320 3.120 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 181 " model vdw 2.387 3.120 nonbonded pdb=" N VAL C 43 " pdb=" OP1 DA I 113 " model vdw 2.390 3.120 nonbonded pdb=" NH2 ARG C 29 " pdb=" OP1 DC I 123 " model vdw 2.406 3.120 ... (remaining 101019 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 45 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 122) } 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=0.00 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.009 0.047 12971 Z= 0.689 Angle : 0.872 9.708 18771 Z= 0.746 Chirality : 0.055 0.466 2136 Planarity : 0.004 0.044 1370 Dihedral : 27.266 178.941 5602 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.29), residues: 765 helix: 1.58 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 17 TYR 0.022 0.002 TYR G 50 PHE 0.013 0.002 PHE B 61 TRP 0.007 0.002 TRP K 176 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.69 (12971) covalent geometry : angle 0.87180 / 0.75 (18771) hydrogen bonds : bond 0.12203 / 8.19 ( 764) hydrogen bonds : angle 3.94054 / 2.90 ( 1913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: D 102 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7726 (pp20) REVERT: G 73 ASN cc_start: 0.8435 (m110) cc_final: 0.8233 (m110) REVERT: H 45 VAL cc_start: 0.8706 (t) cc_final: 0.8469 (m) REVERT: H 73 GLU cc_start: 0.7923 (tp30) cc_final: 0.7574 (tp30) outliers start: 0 outliers final: 1 residues processed: 111 average time/residue: 0.7086 time to fit residues: 83.3393 Evaluate side-chains 68 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 25 ASN G 112 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.054705 restraints weight = 31970.195| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.50 r_work: 0.2795 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12971 Z= 0.156 Angle : 0.671 6.713 18771 Z= 0.394 Chirality : 0.048 0.268 2136 Planarity : 0.004 0.039 1370 Dihedral : 30.421 177.975 4076 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.33 % Allowed : 9.18 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.30), residues: 765 helix: 2.16 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.36 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE B 61 TRP 0.002 0.001 TRP K 176 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.16 (12971) covalent geometry : angle 0.67075 / 0.39 (18771) hydrogen bonds : bond 0.05885 / 3.91 ( 764) hydrogen bonds : angle 3.06212 / 2.23 ( 1913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8357 (tttp) REVERT: D 102 GLU cc_start: 0.8701 (mm-30) cc_final: 0.7895 (pp20) REVERT: H 73 GLU cc_start: 0.8570 (tp30) cc_final: 0.8076 (tp30) outliers start: 15 outliers final: 3 residues processed: 85 average time/residue: 0.6618 time to fit residues: 59.9280 Evaluate side-chains 67 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 97 optimal weight: 10.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054389 restraints weight = 32074.007| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.57 r_work: 0.2781 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12971 Z= 0.205 Angle : 0.697 9.911 18771 Z= 0.400 Chirality : 0.050 0.318 2136 Planarity : 0.005 0.039 1370 Dihedral : 30.798 177.267 4074 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.18 % Allowed : 11.04 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 765 helix: 1.88 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 187 TYR 0.020 0.002 TYR H 39 PHE 0.015 0.002 PHE B 61 TRP 0.002 0.001 TRP K 176 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (12971) covalent geometry : angle 0.69730 / 0.40 (18771) hydrogen bonds : bond 0.06684 / 4.49 ( 764) hydrogen bonds : angle 3.08281 / 2.25 ( 1913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.257 Fit side-chains REVERT: C 72 ASP cc_start: 0.7637 (m-30) cc_final: 0.7353 (m-30) REVERT: D 32 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: D 68 GLU cc_start: 0.8068 (tp30) cc_final: 0.7534 (mt-10) REVERT: E 59 GLU cc_start: 0.8052 (pm20) cc_final: 0.7841 (pm20) REVERT: E 97 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: E 131 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8612 (mtp180) outliers start: 14 outliers final: 4 residues processed: 89 average time/residue: 0.7859 time to fit residues: 73.8091 Evaluate side-chains 72 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054953 restraints weight = 31990.547| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.59 r_work: 0.2800 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12971 Z= 0.151 Angle : 0.637 9.128 18771 Z= 0.369 Chirality : 0.047 0.300 2136 Planarity : 0.004 0.034 1370 Dihedral : 30.742 178.474 4074 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 12.29 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.30), residues: 765 helix: 2.33 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.22 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 63 TYR 0.010 0.001 TYR F 51 PHE 0.011 0.001 PHE E 78 TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (12971) covalent geometry : angle 0.63741 / 0.37 (18771) hydrogen bonds : bond 0.05425 / 3.65 ( 764) hydrogen bonds : angle 2.89032 / 2.10 ( 1913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.207 Fit side-chains REVERT: C 72 ASP cc_start: 0.7425 (m-30) cc_final: 0.7112 (m-30) REVERT: D 32 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: D 68 GLU cc_start: 0.8018 (tp30) cc_final: 0.7587 (mt-10) REVERT: E 76 GLN cc_start: 0.7671 (tp-100) cc_final: 0.7452 (tt0) REVERT: E 131 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8515 (mtp180) outliers start: 13 outliers final: 4 residues processed: 79 average time/residue: 0.7861 time to fit residues: 65.5848 Evaluate side-chains 73 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054973 restraints weight = 31877.006| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.48 r_work: 0.2805 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12971 Z= 0.155 Angle : 0.605 9.226 18771 Z= 0.356 Chirality : 0.045 0.298 2136 Planarity : 0.004 0.034 1370 Dihedral : 30.673 178.825 4074 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.33 % Allowed : 12.60 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.31), residues: 765 helix: 2.60 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 131 TYR 0.008 0.001 TYR F 51 PHE 0.011 0.001 PHE F 61 TRP 0.003 0.001 TRP K 176 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12971) covalent geometry : angle 0.60477 / 0.36 (18771) hydrogen bonds : bond 0.05256 / 3.52 ( 764) hydrogen bonds : angle 2.75538 / 2.00 ( 1913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.336 Fit side-chains REVERT: A 59 GLU cc_start: 0.8042 (pt0) cc_final: 0.7826 (pm20) REVERT: D 68 GLU cc_start: 0.8213 (tp30) cc_final: 0.8011 (mt-10) REVERT: E 131 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8559 (mtp180) REVERT: H 65 ASP cc_start: 0.8762 (t0) cc_final: 0.8552 (t0) outliers start: 15 outliers final: 4 residues processed: 83 average time/residue: 0.8089 time to fit residues: 71.0467 Evaluate side-chains 75 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 78 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055271 restraints weight = 32016.984| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.51 r_work: 0.2809 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12971 Z= 0.144 Angle : 0.586 8.502 18771 Z= 0.344 Chirality : 0.044 0.314 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.646 179.319 4074 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.56 % Allowed : 14.46 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.31), residues: 765 helix: 2.76 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.95 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.001 PHE B 61 TRP 0.003 0.001 TRP K 176 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (12971) covalent geometry : angle 0.58615 / 0.34 (18771) hydrogen bonds : bond 0.04875 / 3.27 ( 764) hydrogen bonds : angle 2.69647 / 1.96 ( 1913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.316 Fit side-chains REVERT: A 59 GLU cc_start: 0.8077 (pt0) cc_final: 0.7877 (pm20) REVERT: C 72 ASP cc_start: 0.7375 (m-30) cc_final: 0.6997 (m-30) REVERT: D 65 ASP cc_start: 0.9385 (t0) cc_final: 0.9099 (t0) REVERT: D 90 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: E 76 GLN cc_start: 0.8093 (tt0) cc_final: 0.7694 (tp-100) REVERT: E 97 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: E 131 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8564 (mtp180) REVERT: H 65 ASP cc_start: 0.8814 (t0) cc_final: 0.8596 (t0) REVERT: K 187 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8049 (ttm170) outliers start: 10 outliers final: 4 residues processed: 84 average time/residue: 0.8049 time to fit residues: 71.5460 Evaluate side-chains 81 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055155 restraints weight = 32036.115| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.51 r_work: 0.2805 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12971 Z= 0.147 Angle : 0.583 9.621 18771 Z= 0.343 Chirality : 0.043 0.315 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.608 179.167 4074 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.87 % Allowed : 13.84 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.31), residues: 765 helix: 2.80 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.008 0.001 TYR F 51 PHE 0.010 0.001 PHE F 61 TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12971) covalent geometry : angle 0.58273 / 0.34 (18771) hydrogen bonds : bond 0.05001 / 3.35 ( 764) hydrogen bonds : angle 2.67716 / 1.94 ( 1913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.234 Fit side-chains REVERT: A 59 GLU cc_start: 0.8117 (pt0) cc_final: 0.7913 (pm20) REVERT: C 72 ASP cc_start: 0.7273 (m-30) cc_final: 0.6884 (m-30) REVERT: D 65 ASP cc_start: 0.9391 (t0) cc_final: 0.9063 (t0) REVERT: D 90 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: E 77 ASP cc_start: 0.8241 (t0) cc_final: 0.7643 (m-30) REVERT: E 97 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: E 131 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8541 (mtp180) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 0.8027 time to fit residues: 67.9938 Evaluate side-chains 82 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054636 restraints weight = 31846.847| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.49 r_work: 0.2790 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12971 Z= 0.156 Angle : 0.594 7.380 18771 Z= 0.346 Chirality : 0.044 0.318 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.638 178.565 4074 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.56 % Allowed : 14.46 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.31), residues: 765 helix: 2.81 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 17 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE B 61 TRP 0.005 0.001 TRP K 176 HIS 0.001 0.000 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (12971) covalent geometry : angle 0.59443 / 0.35 (18771) hydrogen bonds : bond 0.05119 / 3.44 ( 764) hydrogen bonds : angle 2.69469 / 1.96 ( 1913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.233 Fit side-chains REVERT: A 59 GLU cc_start: 0.8185 (pt0) cc_final: 0.7969 (pm20) REVERT: C 72 ASP cc_start: 0.7205 (m-30) cc_final: 0.6857 (m-30) REVERT: D 65 ASP cc_start: 0.9381 (t0) cc_final: 0.9051 (t0) REVERT: E 59 GLU cc_start: 0.8465 (pm20) cc_final: 0.8245 (pm20) REVERT: E 76 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7670 (tp-100) REVERT: E 97 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8238 (mp0) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.7396 time to fit residues: 64.3210 Evaluate side-chains 80 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054620 restraints weight = 31667.593| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.50 r_work: 0.2790 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12971 Z= 0.156 Angle : 0.598 10.698 18771 Z= 0.347 Chirality : 0.044 0.317 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.641 178.538 4074 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 14.77 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.31), residues: 765 helix: 2.81 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.009 0.001 TYR F 51 PHE 0.011 0.001 PHE E 78 TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (12971) covalent geometry : angle 0.59779 / 0.35 (18771) hydrogen bonds : bond 0.05112 / 3.43 ( 764) hydrogen bonds : angle 2.69833 / 1.96 ( 1913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.249 Fit side-chains REVERT: A 59 GLU cc_start: 0.8194 (pt0) cc_final: 0.7975 (pm20) REVERT: C 72 ASP cc_start: 0.7193 (m-30) cc_final: 0.6843 (m-30) REVERT: D 65 ASP cc_start: 0.9385 (t0) cc_final: 0.9055 (t0) REVERT: E 76 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7672 (tp-100) REVERT: E 97 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: E 131 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8249 (mtp180) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.7912 time to fit residues: 65.2049 Evaluate side-chains 81 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054722 restraints weight = 31811.164| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.50 r_work: 0.2792 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12971 Z= 0.145 Angle : 0.596 10.927 18771 Z= 0.346 Chirality : 0.043 0.317 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.642 178.538 4074 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 15.09 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.31), residues: 765 helix: 2.82 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.83 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE F 61 TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (12971) covalent geometry : angle 0.59593 / 0.35 (18771) hydrogen bonds : bond 0.05067 / 3.40 ( 764) hydrogen bonds : angle 2.69775 / 1.96 ( 1913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.196 Fit side-chains REVERT: A 59 GLU cc_start: 0.8193 (pt0) cc_final: 0.7975 (pm20) REVERT: C 72 ASP cc_start: 0.7194 (m-30) cc_final: 0.6847 (m-30) REVERT: D 65 ASP cc_start: 0.9386 (t0) cc_final: 0.9061 (t0) REVERT: E 76 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7687 (tp-100) REVERT: E 97 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: E 131 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8300 (mtp180) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.7719 time to fit residues: 63.7390 Evaluate side-chains 82 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 8 optimal weight: 0.4980 chunk 87 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054705 restraints weight = 31907.987| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.50 r_work: 0.2792 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12971 Z= 0.151 Angle : 0.594 11.484 18771 Z= 0.346 Chirality : 0.043 0.317 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.639 178.513 4074 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 14.93 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.31), residues: 765 helix: 2.81 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE E 78 TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12971) covalent geometry : angle 0.59443 / 0.35 (18771) hydrogen bonds : bond 0.05073 / 3.40 ( 764) hydrogen bonds : angle 2.69029 / 1.95 ( 1913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3083.87 seconds wall clock time: 53 minutes 1.17 seconds (3181.17 seconds total)