Starting phenix.real_space_refine on Thu Mar 5 03:00:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7af8_11756/03_2026/7af8_11756_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7af8_11756/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7af8_11756/03_2026/7af8_11756_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7af8_11756/03_2026/7af8_11756_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7af8_11756/03_2026/7af8_11756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7af8_11756/03_2026/7af8_11756.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.97, per 1000 atoms: 0.21 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: 1.31 Conformation dependent library (CDL) restraints added in 431.9 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: 2.41 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: 4.32 Time building geometry restraints manager: 1.74 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: 28334 2.03 - 4.05: 549 4.05 - 6.08: 56 6.08 - 8.11: 13 8.11 - 10.13: 4 Bond angle restraints: 28956 Sorted by residual: 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 angle pdb=" N PHE B 126 " pdb=" CA PHE B 126 " pdb=" C PHE B 126 " ideal model delta sigma weight residual 111.82 106.72 5.10 1.16e+00 7.43e-01 1.94e+01 angle pdb=" CA GLY B 124 " pdb=" C GLY B 124 " pdb=" O GLY B 124 " ideal model delta sigma weight residual 121.30 117.03 4.27 9.80e-01 1.04e+00 1.90e+01 angle pdb=" N GLY G 55 " pdb=" CA GLY G 55 " pdb=" C GLY G 55 " ideal model delta sigma weight residual 114.90 108.20 6.70 1.54e+00 4.22e-01 1.90e+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: 3376 0.080 - 0.160: 197 0.160 - 0.240: 29 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: 0.010 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.610 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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= 0.292 Angle : 0.634 10.133 28956 Z= 0.410 Chirality : 0.042 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 covalent geometry : bond 0.00450 (19806) covalent geometry : angle 0.63390 (28956) hydrogen bonds : bond 0.17623 ( 813) hydrogen bonds : angle 5.95069 ( 1893) metal coordination : bond 0.15094 ( 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 : 0.278 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: 0.7176 (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: 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: 0.5924 time to fit residues: 186.8280 Evaluate side-chains 223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 227 GLN C 6 HIS C 32 ASN C 102 ASN C 140 ASN I 4 ASN I 37 GLN J 64 GLN J 99 GLN M 52 GLN N 43 ASN N 62 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056684 restraints weight = 45521.317| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.83 r_work: 0.2735 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19807 Z= 0.297 Angle : 0.635 8.896 28956 Z= 0.336 Chirality : 0.042 0.275 3610 Planarity : 0.005 0.047 1996 Dihedral : 21.949 178.002 8375 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.69 % Allowed : 17.48 % Favored : 78.83 % 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: 0.15 (0.25), residues: 1093 helix: 0.99 (0.23), residues: 507 sheet: 0.10 (0.39), residues: 172 loop : -0.95 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 136 TYR 0.012 0.002 TYR C 42 PHE 0.015 0.002 PHE S 74 TRP 0.011 0.001 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00593 (19806) covalent geometry : angle 0.63491 (28956) hydrogen bonds : bond 0.04967 ( 813) hydrogen bonds : angle 3.71889 ( 1893) metal coordination : bond 0.00131 ( 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 258 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8339 (tttt) cc_final: 0.8139 (tptp) REVERT: B 116 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8116 (p0) REVERT: B 118 GLU cc_start: 0.7675 (pt0) cc_final: 0.7305 (pt0) REVERT: B 164 ILE cc_start: 0.7407 (mm) cc_final: 0.6887 (pt) REVERT: B 169 GLU cc_start: 0.7751 (mp0) cc_final: 0.7387 (mp0) REVERT: G 21 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7178 (mp0) REVERT: G 73 VAL cc_start: 0.8634 (p) cc_final: 0.8415 (t) REVERT: I 91 ASP cc_start: 0.8390 (t70) cc_final: 0.7959 (OUTLIER) REVERT: J 89 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8282 (ppt-90) REVERT: M 7 ILE cc_start: 0.9163 (pp) cc_final: 0.8945 (pp) REVERT: M 78 LYS cc_start: 0.8910 (tptm) cc_final: 0.8585 (tptp) REVERT: M 82 ASP cc_start: 0.8623 (m-30) cc_final: 0.8343 (m-30) REVERT: S 21 LYS cc_start: 0.9126 (tptt) cc_final: 0.8883 (tptp) outliers start: 34 outliers final: 13 residues processed: 239 average time/residue: 0.5934 time to fit residues: 158.6381 Evaluate side-chains 216 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 C residue 63 SER 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 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: chunk 149 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN I 4 ASN I 32 GLN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056410 restraints weight = 46014.982| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.74 r_work: 0.2722 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19807 Z= 0.303 Angle : 0.627 9.900 28956 Z= 0.330 Chirality : 0.041 0.235 3610 Planarity : 0.005 0.039 1996 Dihedral : 21.912 178.388 8375 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 4.45 % Allowed : 18.78 % Favored : 76.76 % 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: 0.48 (0.25), residues: 1093 helix: 1.21 (0.23), residues: 512 sheet: 0.23 (0.39), residues: 178 loop : -0.73 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 136 TYR 0.013 0.002 TYR C 42 PHE 0.012 0.001 PHE S 74 TRP 0.012 0.002 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00605 (19806) covalent geometry : angle 0.62749 (28956) hydrogen bonds : bond 0.04862 ( 813) hydrogen bonds : angle 3.70514 ( 1893) metal coordination : bond 0.00072 ( 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 259 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7572 (mm) cc_final: 0.6873 (pp) REVERT: B 82 ASP cc_start: 0.8117 (p0) cc_final: 0.7856 (p0) REVERT: B 118 GLU cc_start: 0.7672 (pt0) cc_final: 0.7326 (pt0) REVERT: B 164 ILE cc_start: 0.7471 (mm) cc_final: 0.6926 (pt) REVERT: B 169 GLU cc_start: 0.7837 (mp0) cc_final: 0.7439 (mp0) REVERT: G 21 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7224 (mp0) REVERT: G 73 VAL cc_start: 0.8592 (p) cc_final: 0.8381 (t) REVERT: I 91 ASP cc_start: 0.8443 (t70) cc_final: 0.7923 (t0) REVERT: I 127 PHE cc_start: 0.9163 (t80) cc_final: 0.8864 (t80) REVERT: J 80 THR cc_start: 0.7665 (m) cc_final: 0.7377 (m) REVERT: J 89 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: M 50 GLU cc_start: 0.8052 (tp30) cc_final: 0.7690 (tp30) REVERT: M 78 LYS cc_start: 0.8874 (tptm) cc_final: 0.8647 (tptp) REVERT: S 32 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8423 (mtp85) outliers start: 41 outliers final: 21 residues processed: 239 average time/residue: 0.6324 time to fit residues: 168.5812 Evaluate side-chains 225 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 186 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain G residue 113 ASP 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 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 25 SER 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: chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3448 r_free = 0.3448 target = 0.083750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059817 restraints weight = 45949.916| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.76 r_work: 0.2812 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19807 Z= 0.137 Angle : 0.555 8.212 28956 Z= 0.293 Chirality : 0.036 0.218 3610 Planarity : 0.004 0.041 1996 Dihedral : 21.902 179.506 8375 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 3.80 % Allowed : 21.28 % Favored : 74.92 % 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: 0.74 (0.25), residues: 1093 helix: 1.40 (0.23), residues: 512 sheet: 0.49 (0.39), residues: 178 loop : -0.63 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 136 TYR 0.012 0.001 TYR C 42 PHE 0.010 0.001 PHE S 74 TRP 0.014 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00275 (19806) covalent geometry : angle 0.55525 (28956) hydrogen bonds : bond 0.04105 ( 813) hydrogen bonds : angle 3.55205 ( 1893) metal coordination : bond 0.00008 ( 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 262 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7632 (mm) cc_final: 0.6898 (pp) REVERT: B 69 PHE cc_start: 0.6303 (m-80) cc_final: 0.5886 (m-80) REVERT: B 82 ASP cc_start: 0.8106 (p0) cc_final: 0.7846 (p0) REVERT: B 118 GLU cc_start: 0.7533 (pt0) cc_final: 0.7140 (pt0) REVERT: B 164 ILE cc_start: 0.7380 (mm) cc_final: 0.6707 (pp) REVERT: B 169 GLU cc_start: 0.7716 (mp0) cc_final: 0.7327 (mp0) REVERT: G 21 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7197 (mp0) REVERT: G 73 VAL cc_start: 0.8642 (p) cc_final: 0.8430 (t) REVERT: G 116 MET cc_start: 0.7231 (tpt) cc_final: 0.6885 (tpp) REVERT: I 91 ASP cc_start: 0.8347 (t70) cc_final: 0.7831 (t0) REVERT: I 127 PHE cc_start: 0.9042 (t80) cc_final: 0.8783 (t80) REVERT: J 88 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8271 (ptp) REVERT: J 89 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8234 (ppt-90) REVERT: M 50 GLU cc_start: 0.8022 (tp30) cc_final: 0.7785 (tp30) REVERT: M 78 LYS cc_start: 0.8897 (tptm) cc_final: 0.8586 (tptp) REVERT: S 32 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8342 (mtp85) outliers start: 35 outliers final: 16 residues processed: 245 average time/residue: 0.5892 time to fit residues: 161.9359 Evaluate side-chains 233 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 210 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL 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 88 MET Chi-restraints excluded: chain J residue 89 ARG Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 63 optimal weight: 30.0000 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 140 ASN I 4 ASN I 37 GLN I 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057300 restraints weight = 45578.876| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.70 r_work: 0.2745 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19807 Z= 0.261 Angle : 0.603 8.273 28956 Z= 0.317 Chirality : 0.039 0.208 3610 Planarity : 0.005 0.039 1996 Dihedral : 21.853 179.476 8375 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 4.23 % Allowed : 23.13 % Favored : 72.64 % 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: 0.80 (0.26), residues: 1093 helix: 1.46 (0.23), residues: 512 sheet: 0.53 (0.39), residues: 178 loop : -0.62 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 119 TYR 0.014 0.002 TYR C 42 PHE 0.027 0.002 PHE B 91 TRP 0.011 0.001 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00525 (19806) covalent geometry : angle 0.60318 (28956) hydrogen bonds : bond 0.04464 ( 813) hydrogen bonds : angle 3.59021 ( 1893) metal coordination : bond 0.00029 ( 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 254 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7744 (mm) cc_final: 0.7004 (pp) REVERT: B 82 ASP cc_start: 0.8098 (p0) cc_final: 0.7854 (p0) REVERT: B 118 GLU cc_start: 0.7367 (pt0) cc_final: 0.7027 (pt0) REVERT: B 164 ILE cc_start: 0.7420 (mm) cc_final: 0.6897 (pp) REVERT: B 169 GLU cc_start: 0.7770 (mp0) cc_final: 0.7333 (mp0) REVERT: G 21 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7228 (mp0) REVERT: I 91 ASP cc_start: 0.8421 (t70) cc_final: 0.7873 (t0) REVERT: M 59 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8541 (mm-30) REVERT: M 78 LYS cc_start: 0.8856 (tptm) cc_final: 0.8630 (tptp) REVERT: S 21 LYS cc_start: 0.8983 (ttmp) cc_final: 0.8623 (tptp) REVERT: S 24 GLU cc_start: 0.8835 (pp20) cc_final: 0.8600 (pp20) outliers start: 39 outliers final: 21 residues processed: 238 average time/residue: 0.6284 time to fit residues: 167.1172 Evaluate side-chains 229 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 113 ASP 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 80 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 19 VAL 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: chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3443 r_free = 0.3443 target = 0.083570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059634 restraints weight = 45356.079| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.75 r_work: 0.2806 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19807 Z= 0.150 Angle : 0.564 9.960 28956 Z= 0.296 Chirality : 0.036 0.203 3610 Planarity : 0.004 0.043 1996 Dihedral : 21.861 179.918 8375 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 3.91 % Allowed : 24.00 % Favored : 72.10 % 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: 0.90 (0.25), residues: 1093 helix: 1.55 (0.23), residues: 512 sheet: 0.63 (0.39), residues: 178 loop : -0.62 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 89 TYR 0.014 0.001 TYR C 42 PHE 0.028 0.001 PHE B 91 TRP 0.014 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00305 (19806) covalent geometry : angle 0.56377 (28956) hydrogen bonds : bond 0.04048 ( 813) hydrogen bonds : angle 3.47897 ( 1893) metal coordination : bond 0.00214 ( 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 262 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7661 (mm) cc_final: 0.7176 (pp) REVERT: B 82 ASP cc_start: 0.8053 (p0) cc_final: 0.7839 (p0) REVERT: B 118 GLU cc_start: 0.7370 (pt0) cc_final: 0.7112 (pt0) REVERT: B 164 ILE cc_start: 0.7304 (mm) cc_final: 0.6720 (pp) REVERT: B 169 GLU cc_start: 0.7667 (mp0) cc_final: 0.7300 (mp0) REVERT: G 21 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7245 (mp0) REVERT: G 106 GLU cc_start: 0.8913 (tt0) cc_final: 0.8356 (pp20) REVERT: G 110 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8194 (mtmt) REVERT: G 116 MET cc_start: 0.7206 (tpt) cc_final: 0.6926 (tpp) REVERT: I 91 ASP cc_start: 0.8408 (t70) cc_final: 0.7945 (t0) REVERT: I 127 PHE cc_start: 0.9116 (t80) cc_final: 0.8885 (t80) REVERT: J 30 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8737 (mmpt) REVERT: J 88 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8312 (ptp) REVERT: J 89 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8219 (ppt-90) REVERT: M 59 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8560 (mm-30) REVERT: M 78 LYS cc_start: 0.8856 (tptm) cc_final: 0.8611 (tptp) REVERT: M 82 ASP cc_start: 0.8610 (m-30) cc_final: 0.8381 (m-30) REVERT: N 34 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8639 (m) REVERT: S 21 LYS cc_start: 0.8962 (ttmp) cc_final: 0.8696 (tptt) REVERT: S 65 GLU cc_start: 0.8815 (tp30) cc_final: 0.8250 (tp30) outliers start: 36 outliers final: 18 residues processed: 247 average time/residue: 0.6288 time to fit residues: 174.0535 Evaluate side-chains 234 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 194 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL 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 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 88 MET Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.0020 chunk 38 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 140 ASN C 185 ASN I 4 ASN I 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061021 restraints weight = 45489.120| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.72 r_work: 0.2840 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19807 Z= 0.132 Angle : 0.563 10.150 28956 Z= 0.295 Chirality : 0.035 0.199 3610 Planarity : 0.004 0.047 1996 Dihedral : 21.845 179.373 8375 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 4.02 % Allowed : 24.76 % Favored : 71.23 % 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: 0.85 (0.25), residues: 1093 helix: 1.50 (0.23), residues: 512 sheet: 0.62 (0.39), residues: 180 loop : -0.65 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 89 TYR 0.017 0.001 TYR C 42 PHE 0.024 0.001 PHE B 91 TRP 0.014 0.001 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00276 (19806) covalent geometry : angle 0.56253 (28956) hydrogen bonds : bond 0.03927 ( 813) hydrogen bonds : angle 3.48258 ( 1893) metal coordination : bond 0.00053 ( 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 261 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ILE cc_start: 0.7673 (mm) cc_final: 0.7009 (pp) REVERT: B 82 ASP cc_start: 0.8249 (p0) cc_final: 0.8017 (p0) REVERT: B 118 GLU cc_start: 0.7398 (pt0) cc_final: 0.7130 (pt0) REVERT: B 164 ILE cc_start: 0.7295 (mm) cc_final: 0.6844 (pp) REVERT: G 13 LEU cc_start: 0.7995 (mp) cc_final: 0.7791 (mt) REVERT: G 21 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7213 (mp0) REVERT: G 48 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5768 (mm-30) REVERT: G 106 GLU cc_start: 0.8886 (tt0) cc_final: 0.8383 (pp20) REVERT: I 91 ASP cc_start: 0.8296 (t70) cc_final: 0.7866 (t0) REVERT: M 59 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8647 (mm-30) REVERT: M 78 LYS cc_start: 0.8857 (tptm) cc_final: 0.8635 (tptp) REVERT: N 34 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8579 (m) REVERT: S 21 LYS cc_start: 0.8965 (ttmp) cc_final: 0.8665 (tptt) REVERT: S 24 GLU cc_start: 0.8827 (pp20) cc_final: 0.8575 (pp20) REVERT: S 65 GLU cc_start: 0.8773 (tp30) cc_final: 0.8128 (tp30) outliers start: 37 outliers final: 20 residues processed: 246 average time/residue: 0.5729 time to fit residues: 158.8798 Evaluate side-chains 231 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 SER 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 J residue 52 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 92 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 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 19 VAL 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: chunk 39 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 64 optimal weight: 40.0000 chunk 144 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 140 ASN I 4 ASN I 37 GLN J 58 ASN J 70 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058251 restraints weight = 44904.804| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.70 r_work: 0.2771 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19807 Z= 0.224 Angle : 0.618 10.071 28956 Z= 0.320 Chirality : 0.038 0.197 3610 Planarity : 0.005 0.044 1996 Dihedral : 21.808 179.824 8375 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 3.91 % Allowed : 26.28 % Favored : 69.82 % 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: 0.81 (0.26), residues: 1093 helix: 1.45 (0.23), residues: 512 sheet: 0.67 (0.40), residues: 178 loop : -0.67 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 32 TYR 0.015 0.002 TYR C 42 PHE 0.033 0.002 PHE I 127 TRP 0.009 0.001 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00461 (19806) covalent geometry : angle 0.61752 (28956) hydrogen bonds : bond 0.04273 ( 813) hydrogen bonds : angle 3.59270 ( 1893) metal coordination : bond 0.00068 ( 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 250 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: B 118 GLU cc_start: 0.7322 (pt0) cc_final: 0.7050 (pt0) REVERT: B 137 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6783 (mmt-90) REVERT: B 159 ASP cc_start: 0.7637 (p0) cc_final: 0.7391 (p0) REVERT: G 13 LEU cc_start: 0.7987 (mp) cc_final: 0.7768 (mt) REVERT: G 21 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7258 (mp0) REVERT: G 106 GLU cc_start: 0.8885 (tt0) cc_final: 0.8246 (pp20) REVERT: I 91 ASP cc_start: 0.8404 (t70) cc_final: 0.7924 (t0) REVERT: J 30 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8748 (mmpt) REVERT: J 89 ARG cc_start: 0.8556 (ttp-170) cc_final: 0.8165 (ttp80) REVERT: M 78 LYS cc_start: 0.8834 (tptm) cc_final: 0.8620 (tptp) REVERT: M 82 ASP cc_start: 0.8665 (m-30) cc_final: 0.8464 (m-30) REVERT: S 21 LYS cc_start: 0.8962 (ttmp) cc_final: 0.8661 (tptt) REVERT: S 24 GLU cc_start: 0.8830 (pp20) cc_final: 0.8582 (pp20) REVERT: S 65 GLU cc_start: 0.8786 (tp30) cc_final: 0.8149 (tp30) outliers start: 36 outliers final: 22 residues processed: 236 average time/residue: 0.5943 time to fit residues: 157.7187 Evaluate side-chains 229 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 SER 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 72 ILE 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 92 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 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 61 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 185 ASN I 4 ASN I 32 GLN I 37 GLN J 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059035 restraints weight = 45199.008| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.71 r_work: 0.2789 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19807 Z= 0.189 Angle : 0.600 9.575 28956 Z= 0.312 Chirality : 0.037 0.195 3610 Planarity : 0.004 0.048 1996 Dihedral : 21.819 179.654 8375 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.04 % Allowed : 27.69 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1093 helix: 1.46 (0.23), residues: 512 sheet: 0.65 (0.39), residues: 180 loop : -0.64 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 89 TYR 0.016 0.002 TYR I 6 PHE 0.019 0.001 PHE B 91 TRP 0.012 0.001 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00390 (19806) covalent geometry : angle 0.59982 (28956) hydrogen bonds : bond 0.04073 ( 813) hydrogen bonds : angle 3.62060 ( 1893) metal coordination : bond 0.00053 ( 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 234 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.5521 (mmp) cc_final: 0.4333 (mtp) REVERT: B 82 ASP cc_start: 0.8635 (p0) cc_final: 0.8302 (p0) REVERT: B 118 GLU cc_start: 0.7304 (pt0) cc_final: 0.7030 (pt0) REVERT: B 159 ASP cc_start: 0.7619 (p0) cc_final: 0.7404 (p0) REVERT: G 21 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7232 (mp0) REVERT: G 116 MET cc_start: 0.7128 (tpt) cc_final: 0.6582 (tpp) REVERT: I 42 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8120 (mm-30) REVERT: I 91 ASP cc_start: 0.8357 (t70) cc_final: 0.7860 (t0) REVERT: I 127 PHE cc_start: 0.9007 (t80) cc_final: 0.8803 (t80) REVERT: J 88 MET cc_start: 0.8719 (tpp) cc_final: 0.8453 (ptt) REVERT: J 89 ARG cc_start: 0.8618 (ttp-170) cc_final: 0.8189 (ttp80) REVERT: M 54 ASP cc_start: 0.8507 (m-30) cc_final: 0.8271 (p0) REVERT: M 59 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8572 (mm-30) REVERT: M 78 LYS cc_start: 0.8870 (tptm) cc_final: 0.8623 (tptp) REVERT: S 21 LYS cc_start: 0.8971 (ttmp) cc_final: 0.8674 (tptt) REVERT: S 24 GLU cc_start: 0.8828 (pp20) cc_final: 0.8626 (pp20) REVERT: S 65 GLU cc_start: 0.8769 (tp30) cc_final: 0.8086 (tp30) outliers start: 28 outliers final: 21 residues processed: 224 average time/residue: 0.5915 time to fit residues: 148.7942 Evaluate side-chains 222 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain C residue 63 SER 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 72 ILE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 92 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 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS B 146 ASN C 140 ASN I 4 ASN I 37 GLN J 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057890 restraints weight = 44952.309| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.69 r_work: 0.2760 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19807 Z= 0.234 Angle : 0.623 11.267 28956 Z= 0.324 Chirality : 0.039 0.213 3610 Planarity : 0.005 0.045 1996 Dihedral : 21.823 179.817 8375 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 2.93 % Allowed : 28.34 % Favored : 68.73 % 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 (0.26), residues: 1093 helix: 1.46 (0.23), residues: 512 sheet: 0.69 (0.40), residues: 178 loop : -0.66 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 45 TYR 0.017 0.002 TYR C 42 PHE 0.019 0.001 PHE B 91 TRP 0.010 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00480 (19806) covalent geometry : angle 0.62334 (28956) hydrogen bonds : bond 0.04251 ( 813) hydrogen bonds : angle 3.67317 ( 1893) metal coordination : bond 0.00046 ( 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 229 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 ASP cc_start: 0.8701 (p0) cc_final: 0.8358 (p0) REVERT: B 118 GLU cc_start: 0.7250 (pt0) cc_final: 0.7044 (pt0) REVERT: B 133 GLU cc_start: 0.8000 (tt0) cc_final: 0.7772 (mt-10) REVERT: B 159 ASP cc_start: 0.7590 (p0) cc_final: 0.7390 (p0) REVERT: G 21 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7111 (mp0) REVERT: I 42 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8172 (mm-30) REVERT: I 91 ASP cc_start: 0.8390 (t70) cc_final: 0.7909 (t0) REVERT: I 127 PHE cc_start: 0.9040 (t80) cc_final: 0.8776 (t80) REVERT: J 30 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8861 (mmpt) REVERT: J 89 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8251 (ttp80) REVERT: M 59 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8721 (tp30) REVERT: M 78 LYS cc_start: 0.8816 (tptm) cc_final: 0.8597 (tptp) REVERT: S 21 LYS cc_start: 0.8992 (ttmp) cc_final: 0.8694 (tptp) REVERT: S 65 GLU cc_start: 0.8768 (tp30) cc_final: 0.8131 (tp30) outliers start: 27 outliers final: 23 residues processed: 220 average time/residue: 0.5721 time to fit residues: 141.8643 Evaluate side-chains 220 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain C residue 63 SER 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 72 ILE 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 92 LEU Chi-restraints excluded: chain M residue 49 SER 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 100 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 56 GLN Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 102 optimal weight: 0.0000 chunk 146 optimal weight: 0.3980 chunk 107 optimal weight: 0.2980 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN I 4 ASN I 37 GLN M 52 GLN N 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.085600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062237 restraints weight = 45692.314| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.78 r_work: 0.2880 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19807 Z= 0.124 Angle : 0.601 17.434 28956 Z= 0.307 Chirality : 0.035 0.230 3610 Planarity : 0.004 0.056 1996 Dihedral : 21.858 178.941 8375 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 2.28 % Allowed : 29.53 % Favored : 68.19 % 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: 0.92 (0.26), residues: 1093 helix: 1.50 (0.23), residues: 512 sheet: 0.70 (0.39), residues: 184 loop : -0.54 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 119 TYR 0.019 0.002 TYR I 6 PHE 0.019 0.001 PHE B 91 TRP 0.017 0.002 TRP N 42 HIS 0.004 0.000 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00266 (19806) covalent geometry : angle 0.60087 (28956) hydrogen bonds : bond 0.03933 ( 813) hydrogen bonds : angle 3.65732 ( 1893) metal coordination : bond 0.00047 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7169.75 seconds wall clock time: 122 minutes 45.86 seconds (7365.86 seconds total)