Starting phenix.real_space_refine on Sun Oct 25 22:08:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7af8_11756/10_2026/7af8_11756_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7af8_11756/10_2026/7af8_11756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7af8_11756/10_2026/7af8_11756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7af8_11756/10_2026/7af8_11756.map" model { file = "/net/cci-nas-00/data/ceres_data/7af8_11756/10_2026/7af8_11756_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7af8_11756/10_2026/7af8_11756_neut.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 51 5.21 5 S 28 5.16 5 C 9848 2.51 5 N 3450 2.21 5 O 4731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18565 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.36, per 1000 atoms: 0.18 Number of scatterers: 18565 At special positions: 0 Unit cell: (114.45, 150.15, 126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 51 11.99 O 4731 8.00 N 3450 7.00 C 9848 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: 1.61 Conformation dependent library (CDL) restraints added in 391.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 50.7% alpha, 15.3% beta 138 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.706A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.580A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.226A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 82 through 96 removed outlier: 3.661A pdb=" N VAL C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.681A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.558A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.756A pdb=" N PHE G 151 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 152 " --> pdb=" O LYS G 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 148 through 152' Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 48 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.816A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 61 removed outlier: 4.136A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.742A pdb=" N LEU M 69 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.605A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 37 through 51 Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 81 through 90 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.722A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.603A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.640A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 78 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 Processing sheet with id=AA7, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AA8, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AA9, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.629A pdb=" N LEU N 79 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 31 through 33 473 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 2.10 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: 2716 1.33 - 1.45: 7337 1.45 - 1.57: 8789 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19806 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.467 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.465 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N VAL J 57 " pdb=" CA VAL J 57 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N THR B 125 " pdb=" CA THR B 125 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.335 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 19801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 27347 2.03 - 4.05: 1536 4.05 - 6.08: 56 6.08 - 8.11: 13 8.11 - 10.13: 4 Bond angle restraints: 28956 Sorted by residual: angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sigma weight residual 118.80 124.43 -5.63 1.10e+00 8.26e-01 2.62e+01 angle pdb=" O4 U 11007 " pdb=" C4 U 11007 " pdb=" C5 U 11007 " ideal model delta sigma weight residual 125.90 128.96 -3.06 6.00e-01 2.78e+00 2.60e+01 angle pdb=" O2 U 11007 " pdb=" C2 U 11007 " pdb=" N3 U 11007 " ideal model delta sigma weight residual 122.20 118.63 3.57 7.00e-01 2.04e+00 2.60e+01 angle pdb=" N ARG J 37 " pdb=" CA ARG J 37 " pdb=" C ARG J 37 " ideal model delta sigma weight residual 110.14 102.36 7.78 1.55e+00 4.16e-01 2.52e+01 angle pdb=" N VAL I 104 " pdb=" CA VAL I 104 " pdb=" C VAL I 104 " ideal model delta sigma weight residual 112.29 107.61 4.68 9.40e-01 1.13e+00 2.48e+01 ... (remaining 28951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 11462 35.62 - 71.24: 1059 71.24 - 106.86: 130 106.86 - 142.48: 1 142.48 - 178.09: 2 Dihedral angle restraints: 12654 sinusoidal: 9481 harmonic: 3173 Sorted by residual: dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 66.75 133.25 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" O4' U 11168 " pdb=" C1' U 11168 " pdb=" N1 U 11168 " pdb=" C2 U 11168 " ideal model delta sinusoidal sigma weight residual 232.00 53.91 178.09 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 65.72 166.28 1 1.70e+01 3.46e-03 6.55e+01 ... (remaining 12651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2978 0.080 - 0.160: 600 0.160 - 0.240: 24 0.240 - 0.320: 6 0.320 - 0.400: 2 Chirality restraints: 3610 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA ASN N 35 " pdb=" N ASN N 35 " pdb=" C ASN N 35 " pdb=" CB ASN N 35 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 3607 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA J 34 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C ALA J 34 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA J 34 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN J 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 103 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C PHE I 103 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE I 103 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL I 104 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.007 2.00e-02 2.50e+03 1.08e-02 3.79e+00 pdb=" N9 2MG 11207 " 0.000 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.006 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.007 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.001 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.001 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.006 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.005 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.011 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.016 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.009 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.002 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.029 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 159 2.58 - 3.16: 14340 3.16 - 3.74: 35039 3.74 - 4.32: 49952 4.32 - 4.90: 68432 Nonbonded interactions: 167922 Sorted by model distance: nonbonded pdb=" OP1 G 1 993 " pdb="MG MG 11604 " model vdw 2.002 2.170 nonbonded pdb=" OP1 G 1 945 " pdb="MG MG 11642 " model vdw 2.004 2.170 nonbonded pdb=" OP2 C 11158 " pdb="MG MG 11637 " model vdw 2.030 2.170 nonbonded pdb=" O6 G 11108 " pdb="MG MG 11626 " model vdw 2.035 2.170 nonbonded pdb=" OP2 U 11085 " pdb="MG MG 11651 " model vdw 2.061 2.170 ... (remaining 167917 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.990 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 0.151 19807 Z= 0.365 Angle : 0.797 10.133 28956 Z= 0.593 Chirality : 0.060 0.400 3610 Planarity : 0.004 0.044 1996 Dihedral : 21.141 178.094 10600 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.39 % 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: -0.93 (0.24), residues: 1093 helix: 0.04 (0.22), residues: 508 sheet: -0.48 (0.38), residues: 173 loop : -1.38 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 106 TYR 0.007 0.001 TYR J 65 PHE 0.009 0.001 PHE B 90 TRP 0.013 0.001 TRP C 201 HIS 0.006 0.001 HIS S 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.36 (19806) covalent geometry : angle 0.79718 / 0.59 (28956) hydrogen bonds : bond 0.17623 / 18.76 ( 813) hydrogen bonds : angle 5.95069 / 8.13 ( 1893) metal coordination : bond 0.15094 / 7.55 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ILE cc_start: 0.8236 (mm) cc_final: 0.7927 (pt) REVERT: G 21 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7177 (mp0) REVERT: G 73 VAL cc_start: 0.8453 (p) cc_final: 0.8150 (t) REVERT: G 139 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7877 (pt0) REVERT: I 91 ASP cc_start: 0.7689 (t70) cc_final: 0.7403 (t0) REVERT: J 30 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8695 (mmpt) REVERT: J 90 LEU cc_start: 0.8878 (tp) cc_final: 0.8510 (OUTLIER) REVERT: M 114 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7908 (mmmt) REVERT: N 34 VAL cc_start: 0.8926 (m) cc_final: 0.8692 (t) outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 0.5764 time to fit residues: 182.9351 Evaluate side-chains 224 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN C 6 HIS C 32 ASN C 102 ASN C 140 ASN I 4 ASN I 37 GLN J 99 GLN M 52 GLN N 35 ASN N 43 ASN N 62 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058128 restraints weight = 45377.031| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.77 r_work: 0.2775 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19807 Z= 0.200 Angle : 0.594 7.985 28956 Z= 0.334 Chirality : 0.043 0.300 3610 Planarity : 0.005 0.056 1996 Dihedral : 21.870 177.136 8375 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.04 % Allowed : 16.94 % Favored : 80.02 % 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: 0.05 (0.25), residues: 1093 helix: 0.87 (0.23), residues: 505 sheet: 0.16 (0.40), residues: 171 loop : -0.99 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.012 0.002 TYR C 42 PHE 0.020 0.002 PHE B 184 TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS S 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 (19806) covalent geometry : angle 0.59427 / 0.33 (28956) hydrogen bonds : bond 0.06185 / 6.77 ( 813) hydrogen bonds : angle 3.83674 / 5.20 ( 1893) metal coordination : bond 0.02045 / 1.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8333 (tttt) cc_final: 0.8107 (tptp) REVERT: B 164 ILE cc_start: 0.7478 (mm) cc_final: 0.7046 (pt) REVERT: B 169 GLU cc_start: 0.7506 (mp0) cc_final: 0.7260 (mp0) REVERT: G 21 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7184 (mp0) REVERT: G 73 VAL cc_start: 0.8670 (p) cc_final: 0.8446 (t) REVERT: I 91 ASP cc_start: 0.8336 (t70) cc_final: 0.7916 (t0) REVERT: J 89 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8315 (ppt-90) REVERT: M 78 LYS cc_start: 0.8917 (tptm) cc_final: 0.8653 (tptp) REVERT: S 21 LYS cc_start: 0.9054 (tptt) cc_final: 0.8753 (tptp) REVERT: S 24 GLU cc_start: 0.8930 (pp20) cc_final: 0.8701 (pp20) REVERT: S 25 SER cc_start: 0.8933 (m) cc_final: 0.8590 (m) outliers start: 28 outliers final: 10 residues processed: 237 average time/residue: 0.5865 time to fit residues: 156.2416 Evaluate side-chains 222 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [149, 2, 125, 40, 124, 115, 63, 43, 152, 61, 44] chunk 149 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 124 optimal weight: 0.0050 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 GLN I 4 ASN I 32 GLN I 37 GLN J 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056769 restraints weight = 45763.094| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.79 r_work: 0.2735 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19807 Z= 0.262 Angle : 0.620 9.948 28956 Z= 0.340 Chirality : 0.045 0.258 3610 Planarity : 0.005 0.043 1996 Dihedral : 21.806 178.560 8375 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.23 % Allowed : 18.68 % Favored : 77.09 % 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: 0.35 (0.25), residues: 1093 helix: 1.08 (0.22), residues: 510 sheet: 0.27 (0.39), residues: 182 loop : -0.81 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 95 TYR 0.014 0.002 TYR C 42 PHE 0.027 0.002 PHE B 198 TRP 0.012 0.002 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.26 (19806) covalent geometry : angle 0.62009 / 0.34 (28956) hydrogen bonds : bond 0.05887 / 6.45 ( 813) hydrogen bonds : angle 3.79786 / 5.08 ( 1893) metal coordination : bond 0.00105 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8062 (mt-10) REVERT: B 59 LYS cc_start: 0.8373 (tttt) cc_final: 0.8149 (tptt) REVERT: B 133 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 164 ILE cc_start: 0.7399 (mm) cc_final: 0.6967 (pt) REVERT: B 169 GLU cc_start: 0.7650 (mp0) cc_final: 0.7352 (mp0) REVERT: G 21 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7202 (mp0) REVERT: G 73 VAL cc_start: 0.8675 (p) cc_final: 0.8467 (t) REVERT: I 91 ASP cc_start: 0.8371 (t70) cc_final: 0.7947 (t0) REVERT: I 127 PHE cc_start: 0.9206 (t80) cc_final: 0.8775 (t80) REVERT: J 89 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8316 (ppt-90) REVERT: M 78 LYS cc_start: 0.8909 (tptm) cc_final: 0.8666 (tptp) REVERT: S 21 LYS cc_start: 0.9116 (tptt) cc_final: 0.8891 (tptt) REVERT: S 24 GLU cc_start: 0.8870 (pp20) cc_final: 0.8658 (pp20) REVERT: S 25 SER cc_start: 0.8910 (m) cc_final: 0.8267 (m) REVERT: S 32 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8525 (ttp-170) outliers start: 39 outliers final: 22 residues processed: 228 average time/residue: 0.6130 time to fit residues: 156.3964 Evaluate side-chains 223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [55, 76, 133, 113, 72, 130, 23, 137, 102, 148, 87] chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 185 ASN I 4 ASN I 37 GLN J 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058954 restraints weight = 45695.483| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.76 r_work: 0.2790 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19807 Z= 0.132 Angle : 0.523 8.697 28956 Z= 0.301 Chirality : 0.038 0.207 3610 Planarity : 0.004 0.039 1996 Dihedral : 21.859 179.140 8375 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 4.23 % Allowed : 20.41 % Favored : 75.35 % 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: 0.57 (0.25), residues: 1093 helix: 1.25 (0.23), residues: 510 sheet: 0.35 (0.39), residues: 183 loop : -0.68 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 119 TYR 0.012 0.002 TYR C 42 PHE 0.021 0.001 PHE B 198 TRP 0.013 0.001 TRP C 201 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (19806) covalent geometry : angle 0.52256 / 0.30 (28956) hydrogen bonds : bond 0.05059 / 5.61 ( 813) hydrogen bonds : angle 3.65339 / 4.87 ( 1893) metal coordination : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 82 ASP cc_start: 0.8031 (p0) cc_final: 0.7741 (p0) REVERT: B 133 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 164 ILE cc_start: 0.7408 (mm) cc_final: 0.6942 (pt) REVERT: B 169 GLU cc_start: 0.7764 (mp0) cc_final: 0.7427 (mp0) REVERT: G 21 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7192 (mp0) REVERT: G 73 VAL cc_start: 0.8637 (p) cc_final: 0.8415 (t) REVERT: I 91 ASP cc_start: 0.8297 (t70) cc_final: 0.7844 (t0) REVERT: J 30 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8691 (mmpt) REVERT: J 80 THR cc_start: 0.7649 (m) cc_final: 0.7433 (m) REVERT: J 89 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (ppt-90) REVERT: M 78 LYS cc_start: 0.8872 (tptm) cc_final: 0.8504 (tptp) REVERT: M 80 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8963 (mt) REVERT: S 24 GLU cc_start: 0.8900 (pp20) cc_final: 0.8689 (pp20) REVERT: S 25 SER cc_start: 0.8883 (m) cc_final: 0.8650 (m) REVERT: S 32 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8474 (ttp-170) outliers start: 39 outliers final: 20 residues processed: 242 average time/residue: 0.5682 time to fit residues: 155.0389 Evaluate side-chains 221 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [63, 2, 11, 120, 128, 31, 29, 90, 138, 28, 7] chunk 63 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.0020 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 overall best weight: 3.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 140 ASN I 4 ASN I 32 GLN I 37 GLN J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056483 restraints weight = 45467.285| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.76 r_work: 0.2724 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 19807 Z= 0.295 Angle : 0.653 9.722 28956 Z= 0.353 Chirality : 0.047 0.220 3610 Planarity : 0.005 0.049 1996 Dihedral : 21.757 178.923 8375 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.99 % Allowed : 21.39 % Favored : 73.62 % 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: 0.54 (0.25), residues: 1093 helix: 1.23 (0.23), residues: 511 sheet: 0.38 (0.39), residues: 183 loop : -0.71 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 63 TYR 0.014 0.002 TYR C 42 PHE 0.022 0.002 PHE I 127 TRP 0.011 0.002 TRP C 201 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.30 (19806) covalent geometry : angle 0.65274 / 0.35 (28956) hydrogen bonds : bond 0.05599 / 6.15 ( 813) hydrogen bonds : angle 3.80566 / 5.08 ( 1893) metal coordination : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7548 (mm) cc_final: 0.6851 (pp) REVERT: B 164 ILE cc_start: 0.7348 (mm) cc_final: 0.6996 (pt) REVERT: G 21 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7245 (mp0) REVERT: G 116 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6634 (tpt) REVERT: I 91 ASP cc_start: 0.8354 (t70) cc_final: 0.7896 (t0) REVERT: J 80 THR cc_start: 0.7731 (m) cc_final: 0.7529 (m) REVERT: J 89 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8300 (ppt-90) REVERT: M 78 LYS cc_start: 0.8880 (tptm) cc_final: 0.8576 (tptp) REVERT: M 81 MET cc_start: 0.8906 (mmm) cc_final: 0.8669 (mtp) REVERT: N 37 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8672 (p) REVERT: S 21 LYS cc_start: 0.9004 (tptp) cc_final: 0.8650 (tptp) REVERT: S 25 SER cc_start: 0.8967 (m) cc_final: 0.8480 (m) REVERT: S 32 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8470 (mtp85) outliers start: 46 outliers final: 23 residues processed: 218 average time/residue: 0.5879 time to fit residues: 144.1793 Evaluate side-chains 212 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [75, 92, 135, 122, 130, 133, 72, 144, 16, 70, 58] chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 185 ASN I 4 ASN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059128 restraints weight = 45443.117| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.80 r_work: 0.2795 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19807 Z= 0.126 Angle : 0.535 9.089 28956 Z= 0.307 Chirality : 0.037 0.182 3610 Planarity : 0.004 0.039 1996 Dihedral : 21.837 179.450 8375 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 4.02 % Allowed : 22.58 % Favored : 73.40 % 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: 0.70 (0.25), residues: 1093 helix: 1.37 (0.23), residues: 510 sheet: 0.50 (0.39), residues: 183 loop : -0.68 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 119 TYR 0.015 0.002 TYR I 6 PHE 0.015 0.001 PHE B 198 TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (19806) covalent geometry : angle 0.53482 / 0.31 (28956) hydrogen bonds : bond 0.04928 / 5.48 ( 813) hydrogen bonds : angle 3.64576 / 4.82 ( 1893) metal coordination : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7590 (mm) cc_final: 0.6906 (pp) REVERT: B 82 ASP cc_start: 0.8117 (p0) cc_final: 0.7851 (p0) REVERT: B 164 ILE cc_start: 0.7320 (mm) cc_final: 0.6887 (pp) REVERT: C 93 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8820 (t0) REVERT: G 21 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7196 (mp0) REVERT: G 116 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6408 (tpt) REVERT: I 91 ASP cc_start: 0.8277 (t70) cc_final: 0.7831 (t0) REVERT: J 83 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8466 (p) REVERT: J 89 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8270 (ppt-90) REVERT: M 78 LYS cc_start: 0.8879 (tptm) cc_final: 0.8575 (tptp) REVERT: M 80 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8959 (mt) REVERT: M 81 MET cc_start: 0.8859 (mmm) cc_final: 0.8651 (mtp) REVERT: M 114 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7889 (ptmt) REVERT: S 65 GLU cc_start: 0.8744 (tp30) cc_final: 0.8281 (tp30) outliers start: 37 outliers final: 18 residues processed: 223 average time/residue: 0.5568 time to fit residues: 140.1208 Evaluate side-chains 219 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [128, 38, 119, 118, 144, 135, 143, 5, 133, 40, 79] chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 133 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 140 ASN I 4 ASN I 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059297 restraints weight = 45671.447| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.79 r_work: 0.2798 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19807 Z= 0.137 Angle : 0.546 9.697 28956 Z= 0.306 Chirality : 0.037 0.191 3610 Planarity : 0.004 0.041 1996 Dihedral : 21.773 179.827 8375 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 4.78 % Allowed : 23.24 % Favored : 71.99 % 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: 0.83 (0.26), residues: 1093 helix: 1.50 (0.23), residues: 510 sheet: 0.58 (0.39), residues: 183 loop : -0.66 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 111 TYR 0.015 0.002 TYR C 42 PHE 0.028 0.001 PHE I 127 TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (19806) covalent geometry : angle 0.54568 / 0.31 (28956) hydrogen bonds : bond 0.04810 / 5.34 ( 813) hydrogen bonds : angle 3.61791 / 4.80 ( 1893) metal coordination : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: B 6 MET cc_start: 0.4844 (mmm) cc_final: 0.2563 (ptm) REVERT: B 67 ILE cc_start: 0.7606 (mm) cc_final: 0.6922 (pp) REVERT: B 82 ASP cc_start: 0.8118 (p0) cc_final: 0.7863 (p0) REVERT: B 135 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8548 (tp) REVERT: B 137 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6892 (mmt-90) REVERT: B 164 ILE cc_start: 0.7323 (mm) cc_final: 0.6907 (pp) REVERT: C 93 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8857 (t0) REVERT: G 21 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7210 (mp0) REVERT: G 116 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6285 (tpp) REVERT: I 91 ASP cc_start: 0.8339 (t70) cc_final: 0.7917 (t0) REVERT: I 127 PHE cc_start: 0.9137 (t80) cc_final: 0.8825 (t80) REVERT: J 30 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8688 (mmpt) REVERT: J 89 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8296 (ppt-90) REVERT: M 78 LYS cc_start: 0.8868 (tptm) cc_final: 0.8585 (tptp) REVERT: M 80 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8964 (mt) REVERT: S 65 GLU cc_start: 0.8745 (tp30) cc_final: 0.8146 (tp30) outliers start: 44 outliers final: 24 residues processed: 232 average time/residue: 0.5637 time to fit residues: 147.8449 Evaluate side-chains 230 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [39, 145, 61, 51, 11, 64, 144, 1, 87, 86, 76] chunk 39 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 140 ASN I 4 ASN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058703 restraints weight = 45438.254| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.70 r_work: 0.2784 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19807 Z= 0.168 Angle : 0.566 9.694 28956 Z= 0.315 Chirality : 0.039 0.190 3610 Planarity : 0.005 0.044 1996 Dihedral : 21.729 179.789 8375 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 4.56 % Allowed : 23.89 % Favored : 71.55 % 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: 0.84 (0.26), residues: 1093 helix: 1.51 (0.23), residues: 510 sheet: 0.64 (0.39), residues: 183 loop : -0.68 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 32 TYR 0.015 0.002 TYR C 42 PHE 0.024 0.001 PHE I 127 TRP 0.012 0.001 TRP G 103 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (19806) covalent geometry : angle 0.56637 / 0.31 (28956) hydrogen bonds : bond 0.04839 / 5.37 ( 813) hydrogen bonds : angle 3.62530 / 4.82 ( 1893) metal coordination : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7640 (mm) cc_final: 0.6940 (pp) REVERT: B 82 ASP cc_start: 0.8127 (p0) cc_final: 0.7871 (p0) REVERT: B 135 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8528 (tp) REVERT: B 137 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6857 (mmt-90) REVERT: B 164 ILE cc_start: 0.7382 (mm) cc_final: 0.6965 (pp) REVERT: C 93 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8815 (t0) REVERT: G 21 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7243 (mp0) REVERT: G 116 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6273 (tpt) REVERT: I 91 ASP cc_start: 0.8417 (t70) cc_final: 0.7943 (t0) REVERT: J 89 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8310 (ppt-90) REVERT: M 59 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8530 (mm-30) REVERT: M 78 LYS cc_start: 0.8867 (tptm) cc_final: 0.8557 (tptp) REVERT: M 80 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8962 (mt) REVERT: S 65 GLU cc_start: 0.8754 (tp30) cc_final: 0.8137 (tp30) outliers start: 42 outliers final: 25 residues processed: 226 average time/residue: 0.5742 time to fit residues: 146.4623 Evaluate side-chains 226 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [61, 99, 112, 31, 62, 84, 121, 137, 124, 13, 6] chunk 61 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 140 ASN C 185 ASN I 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058285 restraints weight = 45612.884| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.70 r_work: 0.2771 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19807 Z= 0.187 Angle : 0.585 10.471 28956 Z= 0.324 Chirality : 0.040 0.187 3610 Planarity : 0.005 0.040 1996 Dihedral : 21.723 179.560 8375 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.78 % Allowed : 24.32 % Favored : 70.90 % 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: 0.84 (0.26), residues: 1093 helix: 1.52 (0.23), residues: 510 sheet: 0.62 (0.39), residues: 183 loop : -0.68 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 32 TYR 0.016 0.002 TYR C 42 PHE 0.011 0.001 PHE B 198 TRP 0.015 0.002 TRP G 103 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (19806) covalent geometry : angle 0.58484 / 0.32 (28956) hydrogen bonds : bond 0.04941 / 5.47 ( 813) hydrogen bonds : angle 3.66519 / 4.86 ( 1893) metal coordination : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7630 (mm) cc_final: 0.6931 (pp) REVERT: B 82 ASP cc_start: 0.8103 (p0) cc_final: 0.7858 (p0) REVERT: B 137 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6844 (mmt-90) REVERT: B 164 ILE cc_start: 0.7422 (mm) cc_final: 0.6939 (pp) REVERT: C 93 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8815 (t0) REVERT: G 21 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7262 (mp0) REVERT: I 91 ASP cc_start: 0.8381 (t70) cc_final: 0.7918 (t0) REVERT: J 30 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8750 (mmpt) REVERT: J 89 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8292 (ppt-90) REVERT: M 59 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8394 (mt-10) REVERT: M 78 LYS cc_start: 0.8860 (tptm) cc_final: 0.8556 (tptp) REVERT: M 80 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9015 (mt) REVERT: M 82 ASP cc_start: 0.8645 (m-30) cc_final: 0.8368 (m-30) REVERT: S 65 GLU cc_start: 0.8797 (tp30) cc_final: 0.8203 (tp30) outliers start: 44 outliers final: 23 residues processed: 230 average time/residue: 0.5505 time to fit residues: 143.3874 Evaluate side-chains 230 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [40, 107, 1, 62, 91, 108, 122, 81, 135, 59, 152] chunk 40 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 135 optimal weight: 0.0980 chunk 59 optimal weight: 0.0270 chunk 152 optimal weight: 0.9990 overall best weight: 0.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 185 ASN I 4 ASN I 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.085190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061480 restraints weight = 45635.122| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.77 r_work: 0.2856 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 19807 Z= 0.117 Angle : 0.540 10.017 28956 Z= 0.303 Chirality : 0.035 0.207 3610 Planarity : 0.004 0.046 1996 Dihedral : 21.791 179.918 8375 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 2.50 % Allowed : 27.25 % Favored : 70.25 % 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: 0.82 (0.25), residues: 1093 helix: 1.49 (0.23), residues: 510 sheet: 0.64 (0.40), residues: 182 loop : -0.68 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 7 TYR 0.013 0.002 TYR C 42 PHE 0.032 0.002 PHE I 127 TRP 0.017 0.002 TRP C 201 HIS 0.008 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (19806) covalent geometry : angle 0.53979 / 0.30 (28956) hydrogen bonds : bond 0.04659 / 5.18 ( 813) hydrogen bonds : angle 3.58558 / 4.78 ( 1893) metal coordination : bond 0.00025 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.4296 (mpm) cc_final: 0.3352 (pmm) REVERT: B 67 ILE cc_start: 0.7629 (mm) cc_final: 0.7245 (pp) REVERT: B 82 ASP cc_start: 0.8011 (p0) cc_final: 0.7788 (p0) REVERT: B 91 PHE cc_start: 0.7947 (p90) cc_final: 0.7743 (p90) REVERT: B 137 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6897 (mmt-90) REVERT: B 159 ASP cc_start: 0.7972 (m-30) cc_final: 0.7771 (p0) REVERT: B 162 PHE cc_start: 0.7040 (t80) cc_final: 0.6521 (m-80) REVERT: B 164 ILE cc_start: 0.7235 (mm) cc_final: 0.6782 (pp) REVERT: C 93 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8788 (t0) REVERT: G 13 LEU cc_start: 0.7817 (mp) cc_final: 0.7598 (mt) REVERT: G 21 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7262 (mp0) REVERT: G 60 GLU cc_start: 0.8223 (mp0) cc_final: 0.7853 (mp0) REVERT: G 106 GLU cc_start: 0.8894 (tt0) cc_final: 0.8406 (pp20) REVERT: I 91 ASP cc_start: 0.8349 (t70) cc_final: 0.7943 (t0) REVERT: J 30 LYS cc_start: 0.9196 (mtpp) cc_final: 0.8750 (mmpt) REVERT: J 88 MET cc_start: 0.8539 (tpp) cc_final: 0.8292 (ptp) REVERT: J 89 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8256 (ppt-90) REVERT: M 43 VAL cc_start: 0.9189 (t) cc_final: 0.8952 (p) REVERT: M 59 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8511 (mt-10) REVERT: M 78 LYS cc_start: 0.8903 (tptm) cc_final: 0.8611 (tptp) REVERT: M 80 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8948 (mt) REVERT: S 12 ASP cc_start: 0.8521 (m-30) cc_final: 0.8319 (m-30) REVERT: S 65 GLU cc_start: 0.8748 (tp30) cc_final: 0.8052 (tp30) outliers start: 23 outliers final: 15 residues processed: 234 average time/residue: 0.5610 time to fit residues: 148.7624 Evaluate side-chains 231 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [37, 7, 55, 91, 89, 102, 146, 107, 101, 110, 45] chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 140 ASN I 4 ASN I 37 GLN J 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061681 restraints weight = 45822.141| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.67 r_work: 0.2854 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19807 Z= 0.125 Angle : 0.555 11.712 28956 Z= 0.309 Chirality : 0.036 0.191 3610 Planarity : 0.004 0.049 1996 Dihedral : 21.747 179.773 8375 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 2.71 % Allowed : 28.34 % Favored : 68.95 % 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: 0.84 (0.26), residues: 1093 helix: 1.52 (0.23), residues: 510 sheet: 0.64 (0.40), residues: 183 loop : -0.71 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.018 0.002 TYR J 65 PHE 0.024 0.002 PHE B 91 TRP 0.018 0.002 TRP B 104 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (19806) covalent geometry : angle 0.55530 / 0.31 (28956) hydrogen bonds : bond 0.04597 / 5.14 ( 813) hydrogen bonds : angle 3.62824 / 4.87 ( 1893) metal coordination : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6801.91 seconds wall clock time: 116 minutes 24.44 seconds (6984.44 seconds total)