Starting phenix.real_space_refine on Thu Mar 5 03:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afk_11768/03_2026/7afk_11768_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afk_11768/03_2026/7afk_11768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7afk_11768/03_2026/7afk_11768_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afk_11768/03_2026/7afk_11768_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afk_11768/03_2026/7afk_11768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afk_11768/03_2026/7afk_11768.map" } resolution = 4.9 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= 0.003 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 12 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 18521 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': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 4.20, per 1000 atoms: 0.23 Number of scatterers: 18521 At special positions: 0 Unit cell: (118.265, 116.095, 159.495, 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 12 11.99 O 4730 8.00 N 3449 7.00 C 9845 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: 1.50 Conformation dependent library (CDL) restraints added in 517.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 48.5% alpha, 14.3% beta 116 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A 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 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: 4.225A 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 6 through 11 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.619A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.573A pdb=" N ALA G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.284A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.663A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.516A pdb=" N SER G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 148 removed outlier: 3.613A pdb=" N ALA G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.996A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix 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 removed outlier: 3.509A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 4.240A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.582A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.624A pdb=" N ILE M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 4.405A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 19 Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 49 Processing helix chain 'N' and resid 50 through 51 No H-bonds generated for 'chain 'N' and resid 50 through 51' Processing helix chain 'N' and resid 52 through 56 Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.898A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 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: 5.721A 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: 6.453A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 58 Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 removed outlier: 5.738A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 removed outlier: 6.419A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 45 through 52 Processing sheet with id=AA8, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.817A pdb=" N LYS N 97 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.318A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 4.15 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: 1.20 - 1.33: 2828 1.33 - 1.45: 7327 1.45 - 1.57: 8682 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.468 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 1.443 1.474 -0.031 8.60e-03 1.35e+04 1.28e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.328 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C SER N 55 " pdb=" N SER N 56 " ideal model delta sigma weight residual 1.330 1.280 0.050 1.47e-02 4.63e+03 1.17e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27743 2.05 - 4.11: 1098 4.11 - 6.16: 88 6.16 - 8.21: 16 8.21 - 10.26: 4 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 113.88 105.93 7.95 1.23e+00 6.61e-01 4.18e+01 angle pdb=" O3' C 11103 " pdb=" C3' C 11103 " pdb=" C2' C 11103 " ideal model delta sigma weight residual 113.70 121.69 -7.99 1.50e+00 4.44e-01 2.83e+01 angle pdb=" O3' A 11157 " pdb=" C3' A 11157 " pdb=" C2' A 11157 " ideal model delta sigma weight residual 109.50 101.96 7.54 1.50e+00 4.44e-01 2.52e+01 angle pdb=" CA SER M 46 " pdb=" C SER M 46 " pdb=" O SER M 46 " ideal model delta sigma weight residual 121.56 116.31 5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N GLY N 68 " pdb=" CA GLY N 68 " pdb=" C GLY N 68 " ideal model delta sigma weight residual 115.72 108.87 6.85 1.51e+00 4.39e-01 2.06e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11184 35.78 - 71.56: 1290 71.56 - 107.34: 169 107.34 - 143.12: 4 143.12 - 178.90: 4 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 33.90 166.10 1 1.50e+01 4.44e-03 8.41e+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 -128.00 50.90 -178.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 232.00 54.69 177.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3191 0.077 - 0.154: 328 0.154 - 0.231: 79 0.231 - 0.308: 9 0.308 - 0.385: 2 Chirality restraints: 3609 Sorted by residual: chirality pdb=" C3' C 11103 " pdb=" C4' C 11103 " pdb=" O3' C 11103 " pdb=" C2' C 11103 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE J 49 " pdb=" N PHE J 49 " pdb=" C PHE J 49 " pdb=" CB PHE J 49 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A 1 969 " pdb=" C4' A 1 969 " pdb=" O3' A 1 969 " pdb=" C2' A 1 969 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.048 2.00e-02 2.50e+03 9.87e-02 3.17e+02 pdb=" N9 2MG 11207 " -0.020 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.052 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.072 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.021 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.051 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.047 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.097 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.142 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.084 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.032 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 26 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C PHE G 26 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE G 26 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL G 27 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 120 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C LEU G 120 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU G 120 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA G 121 " 0.016 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 55 2.20 - 2.87: 7424 2.87 - 3.55: 35090 3.55 - 4.22: 60082 4.22 - 4.90: 80301 Nonbonded interactions: 182952 Sorted by model distance: nonbonded pdb=" O3' U 1 952 " pdb="MG MG 11608 " model vdw 1.519 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11610 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11611 " model vdw 1.659 2.170 nonbonded pdb=" OP2 C 1 972 " pdb="MG MG 11607 " model vdw 1.697 2.170 nonbonded pdb=" OP1 C 11109 " pdb="MG MG 11604 " model vdw 1.732 2.170 ... (remaining 182947 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 group one per residue 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: 3.800 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.790 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.007 0.151 19802 Z= 0.432 Angle : 0.892 10.265 28949 Z= 0.551 Chirality : 0.053 0.385 3609 Planarity : 0.005 0.099 1995 Dihedral : 23.874 178.902 10599 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 42.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.23), residues: 1092 helix: -1.23 (0.22), residues: 480 sheet: -2.30 (0.36), residues: 161 loop : -2.40 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 130 TYR 0.011 0.002 TYR N 20 PHE 0.019 0.002 PHE C 37 TRP 0.012 0.002 TRP S 34 HIS 0.007 0.002 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00702 (19801) covalent geometry : angle 0.89228 (28949) hydrogen bonds : bond 0.27501 ( 698) hydrogen bonds : angle 9.72030 ( 1576) metal coordination : bond 0.15081 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 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: 0 poor density : 241 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LEU cc_start: 0.8915 (tp) cc_final: 0.8538 (pp) REVERT: B 129 LEU cc_start: 0.9250 (mt) cc_final: 0.9006 (tp) REVERT: B 139 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7316 (mtt180) REVERT: B 161 LEU cc_start: 0.7981 (mt) cc_final: 0.6825 (mt) REVERT: B 181 ILE cc_start: 0.8233 (mt) cc_final: 0.7913 (tp) REVERT: C 102 ASN cc_start: 0.9455 (t0) cc_final: 0.9199 (m110) REVERT: C 129 MET cc_start: 0.8870 (mmm) cc_final: 0.8227 (tpp) REVERT: C 150 LYS cc_start: 0.8551 (tttm) cc_final: 0.8065 (tptp) REVERT: C 181 ASP cc_start: 0.9054 (t0) cc_final: 0.8373 (p0) REVERT: C 203 PHE cc_start: 0.9076 (t80) cc_final: 0.8691 (t80) REVERT: G 91 VAL cc_start: 0.7421 (p) cc_final: 0.7212 (p) REVERT: I 32 GLN cc_start: 0.8757 (mm110) cc_final: 0.8547 (mm-40) REVERT: I 57 MET cc_start: 0.9379 (ptm) cc_final: 0.9035 (mmm) REVERT: I 110 GLN cc_start: 0.9585 (pt0) cc_final: 0.8757 (pm20) REVERT: I 112 GLU cc_start: 0.8217 (tt0) cc_final: 0.7750 (mp0) REVERT: J 19 ASP cc_start: 0.9199 (m-30) cc_final: 0.8907 (m-30) REVERT: J 53 ILE cc_start: 0.9180 (pt) cc_final: 0.8948 (tt) REVERT: J 63 ASP cc_start: 0.8579 (t0) cc_final: 0.7666 (t0) REVERT: J 65 TYR cc_start: 0.8477 (m-80) cc_final: 0.8111 (m-80) REVERT: M 27 LYS cc_start: 0.9409 (tppt) cc_final: 0.8780 (tppt) REVERT: M 31 LYS cc_start: 0.9248 (pttm) cc_final: 0.8922 (pttp) REVERT: M 50 GLU cc_start: 0.9519 (pm20) cc_final: 0.9141 (tm-30) REVERT: M 68 ASP cc_start: 0.9530 (m-30) cc_final: 0.9003 (t0) REVERT: M 95 LEU cc_start: 0.8930 (mt) cc_final: 0.8360 (mt) REVERT: N 86 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8748 (mt-10) REVERT: N 101 TRP cc_start: 0.8402 (p90) cc_final: 0.6017 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1722 time to fit residues: 59.7872 Evaluate side-chains 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS B 227 GLN G 122 ASN J 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.031467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.022742 restraints weight = 246208.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.023499 restraints weight = 133700.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.023882 restraints weight = 93209.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.024189 restraints weight = 75921.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.024329 restraints weight = 66237.452| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19802 Z= 0.219 Angle : 0.712 11.123 28949 Z= 0.361 Chirality : 0.039 0.243 3609 Planarity : 0.006 0.058 1995 Dihedral : 24.825 176.988 8374 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 28.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % 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: -1.95 (0.24), residues: 1092 helix: -0.58 (0.22), residues: 507 sheet: -1.79 (0.36), residues: 155 loop : -1.84 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 136 TYR 0.011 0.002 TYR J 65 PHE 0.016 0.002 PHE S 74 TRP 0.013 0.002 TRP B 96 HIS 0.006 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00418 (19801) covalent geometry : angle 0.71231 (28949) hydrogen bonds : bond 0.11763 ( 698) hydrogen bonds : angle 5.58803 ( 1576) metal coordination : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 PHE cc_start: 0.8722 (m-10) cc_final: 0.8491 (m-80) REVERT: B 94 HIS cc_start: 0.8998 (t70) cc_final: 0.8706 (t70) REVERT: C 102 ASN cc_start: 0.9611 (t0) cc_final: 0.9149 (m110) REVERT: C 129 MET cc_start: 0.8844 (mmm) cc_final: 0.8198 (tpp) REVERT: C 142 MET cc_start: 0.9170 (tpp) cc_final: 0.8811 (tpt) REVERT: C 168 TYR cc_start: 0.8101 (t80) cc_final: 0.7745 (t80) REVERT: C 181 ASP cc_start: 0.8940 (t0) cc_final: 0.8276 (p0) REVERT: C 203 PHE cc_start: 0.8935 (t80) cc_final: 0.8529 (t80) REVERT: I 110 GLN cc_start: 0.9474 (pt0) cc_final: 0.8732 (pm20) REVERT: I 112 GLU cc_start: 0.8199 (tt0) cc_final: 0.7512 (mp0) REVERT: I 115 LYS cc_start: 0.9033 (mttt) cc_final: 0.8627 (mttt) REVERT: I 118 LEU cc_start: 0.9520 (mm) cc_final: 0.9308 (mt) REVERT: J 19 ASP cc_start: 0.9258 (m-30) cc_final: 0.8997 (m-30) REVERT: J 63 ASP cc_start: 0.7969 (t0) cc_final: 0.7513 (t0) REVERT: J 67 ILE cc_start: 0.9348 (mm) cc_final: 0.9142 (mm) REVERT: M 12 HIS cc_start: 0.8876 (p90) cc_final: 0.8492 (p-80) REVERT: M 27 LYS cc_start: 0.9336 (tppt) cc_final: 0.8992 (tppt) REVERT: M 47 GLU cc_start: 0.9107 (pt0) cc_final: 0.8895 (mp0) REVERT: M 50 GLU cc_start: 0.9539 (pm20) cc_final: 0.9140 (tm-30) REVERT: M 81 MET cc_start: 0.9079 (mtt) cc_final: 0.8879 (mtt) REVERT: N 47 LYS cc_start: 0.9637 (tmtt) cc_final: 0.9267 (mttt) REVERT: S 66 MET cc_start: 0.9413 (mtp) cc_final: 0.9120 (mtp) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.1667 time to fit residues: 48.6034 Evaluate side-chains 132 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 102 optimal weight: 0.0020 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS C 140 ASN G 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.031172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.022522 restraints weight = 251879.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.023227 restraints weight = 137513.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.023675 restraints weight = 94650.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.023973 restraints weight = 76238.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.024101 restraints weight = 67006.242| |-----------------------------------------------------------------------------| r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19802 Z= 0.209 Angle : 0.659 10.792 28949 Z= 0.332 Chirality : 0.037 0.249 3609 Planarity : 0.005 0.062 1995 Dihedral : 24.674 179.476 8374 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 27.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.24), residues: 1092 helix: -0.30 (0.22), residues: 507 sheet: -1.42 (0.37), residues: 155 loop : -1.60 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 68 TYR 0.012 0.002 TYR J 65 PHE 0.016 0.002 PHE B 184 TRP 0.011 0.002 TRP B 96 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00402 (19801) covalent geometry : angle 0.65876 (28949) hydrogen bonds : bond 0.10950 ( 698) hydrogen bonds : angle 5.29538 ( 1576) metal coordination : bond 0.00239 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8778 (t70) cc_final: 0.8331 (t70) REVERT: C 102 ASN cc_start: 0.9630 (t0) cc_final: 0.9227 (m110) REVERT: C 129 MET cc_start: 0.8808 (mmm) cc_final: 0.8191 (tpp) REVERT: C 142 MET cc_start: 0.9196 (tpp) cc_final: 0.8937 (tpt) REVERT: C 168 TYR cc_start: 0.7991 (t80) cc_final: 0.7573 (t80) REVERT: C 181 ASP cc_start: 0.8936 (t0) cc_final: 0.8362 (p0) REVERT: I 110 GLN cc_start: 0.9472 (pt0) cc_final: 0.8733 (pm20) REVERT: I 112 GLU cc_start: 0.8212 (tt0) cc_final: 0.7602 (mp0) REVERT: I 115 LYS cc_start: 0.8961 (mttt) cc_final: 0.8543 (mttt) REVERT: J 19 ASP cc_start: 0.9289 (m-30) cc_final: 0.9056 (m-30) REVERT: J 63 ASP cc_start: 0.8521 (t0) cc_final: 0.7582 (t0) REVERT: J 66 GLU cc_start: 0.6591 (tm-30) cc_final: 0.6082 (tm-30) REVERT: M 12 HIS cc_start: 0.8878 (p90) cc_final: 0.8471 (p-80) REVERT: M 27 LYS cc_start: 0.9366 (tppt) cc_final: 0.9025 (tppt) REVERT: M 50 GLU cc_start: 0.9520 (pm20) cc_final: 0.9134 (tm-30) REVERT: M 81 MET cc_start: 0.9106 (mtt) cc_final: 0.8866 (mtt) REVERT: N 74 LEU cc_start: 0.9391 (tt) cc_final: 0.9183 (tt) REVERT: S 66 MET cc_start: 0.9338 (mtp) cc_final: 0.9060 (mtp) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1607 time to fit residues: 43.7051 Evaluate side-chains 127 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN J 58 ASN N 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.029529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.021542 restraints weight = 268880.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.022189 restraints weight = 152590.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.022510 restraints weight = 109253.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.022709 restraints weight = 89561.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.022876 restraints weight = 81233.418| |-----------------------------------------------------------------------------| r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 19802 Z= 0.401 Angle : 0.856 7.100 28949 Z= 0.429 Chirality : 0.044 0.239 3609 Planarity : 0.007 0.091 1995 Dihedral : 25.072 179.104 8374 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 41.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.23), residues: 1092 helix: -0.78 (0.21), residues: 503 sheet: -1.52 (0.36), residues: 164 loop : -1.98 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 3 TYR 0.021 0.003 TYR J 65 PHE 0.017 0.003 PHE B 91 TRP 0.013 0.002 TRP B 96 HIS 0.012 0.002 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00756 (19801) covalent geometry : angle 0.85591 (28949) hydrogen bonds : bond 0.13520 ( 698) hydrogen bonds : angle 5.88029 ( 1576) metal coordination : bond 0.01177 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8546 (pp30) REVERT: C 102 ASN cc_start: 0.9602 (t0) cc_final: 0.9240 (m110) REVERT: C 129 MET cc_start: 0.8815 (mmm) cc_final: 0.8292 (tpp) REVERT: C 142 MET cc_start: 0.9205 (tpp) cc_final: 0.8942 (tpt) REVERT: C 168 TYR cc_start: 0.8117 (t80) cc_final: 0.7786 (t80) REVERT: C 181 ASP cc_start: 0.8916 (t0) cc_final: 0.8323 (p0) REVERT: G 104 ILE cc_start: 0.8033 (tp) cc_final: 0.7774 (tp) REVERT: I 112 GLU cc_start: 0.8288 (tt0) cc_final: 0.7548 (mp0) REVERT: J 18 ILE cc_start: 0.9561 (tp) cc_final: 0.9297 (tt) REVERT: J 19 ASP cc_start: 0.9125 (m-30) cc_final: 0.8786 (m-30) REVERT: J 63 ASP cc_start: 0.8642 (t0) cc_final: 0.8190 (t70) REVERT: M 27 LYS cc_start: 0.9387 (tppt) cc_final: 0.9022 (tppt) REVERT: M 81 MET cc_start: 0.9195 (mtt) cc_final: 0.8939 (mtt) REVERT: N 6 MET cc_start: 0.9125 (mmm) cc_final: 0.8918 (mmm) REVERT: N 74 LEU cc_start: 0.9451 (tt) cc_final: 0.9219 (tt) REVERT: N 77 PHE cc_start: 0.9564 (m-10) cc_final: 0.9356 (m-10) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1463 time to fit residues: 34.3207 Evaluate side-chains 112 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 131 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.031518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.023077 restraints weight = 245813.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.023807 restraints weight = 132649.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.024190 restraints weight = 91697.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.024373 restraints weight = 74080.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.024589 restraints weight = 67160.937| |-----------------------------------------------------------------------------| r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19802 Z= 0.202 Angle : 0.661 8.033 28949 Z= 0.336 Chirality : 0.038 0.241 3609 Planarity : 0.006 0.096 1995 Dihedral : 24.728 176.621 8374 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1092 helix: -0.36 (0.22), residues: 508 sheet: -1.22 (0.38), residues: 164 loop : -1.62 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 3 TYR 0.009 0.001 TYR I 6 PHE 0.016 0.002 PHE C 23 TRP 0.020 0.002 TRP N 101 HIS 0.005 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00386 (19801) covalent geometry : angle 0.66103 (28949) hydrogen bonds : bond 0.10621 ( 698) hydrogen bonds : angle 5.36374 ( 1576) metal coordination : bond 0.00306 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8377 (pp30) REVERT: B 203 ASN cc_start: 0.5938 (t0) cc_final: 0.5732 (t0) REVERT: C 102 ASN cc_start: 0.9604 (t0) cc_final: 0.9273 (m110) REVERT: C 129 MET cc_start: 0.8698 (mmm) cc_final: 0.8124 (tpp) REVERT: C 168 TYR cc_start: 0.7968 (t80) cc_final: 0.7751 (t80) REVERT: C 181 ASP cc_start: 0.8875 (t0) cc_final: 0.8329 (p0) REVERT: G 40 GLU cc_start: 0.8523 (pp20) cc_final: 0.8163 (mt-10) REVERT: I 61 LEU cc_start: 0.9699 (mt) cc_final: 0.9450 (pt) REVERT: I 130 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7469 (mtm-85) REVERT: J 19 ASP cc_start: 0.9340 (m-30) cc_final: 0.8986 (m-30) REVERT: J 46 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8357 (mmtp) REVERT: J 63 ASP cc_start: 0.8685 (t0) cc_final: 0.7963 (t70) REVERT: J 65 TYR cc_start: 0.9014 (m-80) cc_final: 0.8394 (m-80) REVERT: J 97 ASP cc_start: 0.8836 (t70) cc_final: 0.8624 (t0) REVERT: M 12 HIS cc_start: 0.8897 (p90) cc_final: 0.8532 (p-80) REVERT: M 27 LYS cc_start: 0.9338 (tppt) cc_final: 0.8986 (tppt) REVERT: M 50 GLU cc_start: 0.9475 (pm20) cc_final: 0.9255 (tm-30) REVERT: N 74 LEU cc_start: 0.9445 (tt) cc_final: 0.9188 (tt) REVERT: S 66 MET cc_start: 0.9152 (mtp) cc_final: 0.8916 (mtp) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1476 time to fit residues: 37.0062 Evaluate side-chains 120 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 40.0000 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.030855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.022639 restraints weight = 252865.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.023393 restraints weight = 136318.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.023775 restraints weight = 93181.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.024021 restraints weight = 75209.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.024208 restraints weight = 67004.006| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19802 Z= 0.257 Angle : 0.698 6.724 28949 Z= 0.354 Chirality : 0.039 0.242 3609 Planarity : 0.006 0.085 1995 Dihedral : 24.740 178.914 8374 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 30.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.25), residues: 1092 helix: -0.28 (0.22), residues: 507 sheet: -1.27 (0.37), residues: 165 loop : -1.53 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 3 TYR 0.011 0.002 TYR J 65 PHE 0.022 0.002 PHE B 50 TRP 0.013 0.002 TRP B 96 HIS 0.006 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00489 (19801) covalent geometry : angle 0.69804 (28949) hydrogen bonds : bond 0.11031 ( 698) hydrogen bonds : angle 5.42766 ( 1576) metal coordination : bond 0.00446 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 THR cc_start: 0.5511 (p) cc_final: 0.5171 (p) REVERT: C 102 ASN cc_start: 0.9604 (t0) cc_final: 0.9271 (m110) REVERT: C 129 MET cc_start: 0.8746 (mmm) cc_final: 0.8196 (tpp) REVERT: C 150 LYS cc_start: 0.8704 (tttm) cc_final: 0.8322 (tptp) REVERT: C 168 TYR cc_start: 0.8062 (t80) cc_final: 0.7245 (t80) REVERT: C 181 ASP cc_start: 0.8867 (t0) cc_final: 0.8329 (p0) REVERT: G 40 GLU cc_start: 0.8532 (pp20) cc_final: 0.8150 (mt-10) REVERT: I 130 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7495 (mtm-85) REVERT: J 63 ASP cc_start: 0.8732 (t0) cc_final: 0.8199 (t70) REVERT: J 97 ASP cc_start: 0.8884 (t70) cc_final: 0.8666 (t0) REVERT: M 12 HIS cc_start: 0.8912 (p90) cc_final: 0.8550 (p-80) REVERT: M 27 LYS cc_start: 0.9357 (tppt) cc_final: 0.9032 (tptt) REVERT: M 81 MET cc_start: 0.9178 (mtt) cc_final: 0.8788 (mmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1532 time to fit residues: 34.7594 Evaluate side-chains 125 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.032327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.023786 restraints weight = 241467.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.024599 restraints weight = 129412.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.025031 restraints weight = 87632.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.025329 restraints weight = 69985.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.025501 restraints weight = 61742.275| |-----------------------------------------------------------------------------| r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19802 Z= 0.157 Angle : 0.622 6.794 28949 Z= 0.318 Chirality : 0.036 0.254 3609 Planarity : 0.005 0.099 1995 Dihedral : 24.488 177.043 8374 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.25), residues: 1092 helix: -0.08 (0.22), residues: 507 sheet: -1.04 (0.38), residues: 167 loop : -1.35 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 10 TYR 0.015 0.001 TYR G 44 PHE 0.021 0.001 PHE C 37 TRP 0.012 0.002 TRP C 201 HIS 0.004 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00305 (19801) covalent geometry : angle 0.62212 (28949) hydrogen bonds : bond 0.10148 ( 698) hydrogen bonds : angle 5.17134 ( 1576) metal coordination : bond 0.00174 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.9472 (tpt170) cc_final: 0.9179 (mtm110) REVERT: B 189 THR cc_start: 0.5501 (p) cc_final: 0.5241 (p) REVERT: C 29 PHE cc_start: 0.9052 (t80) cc_final: 0.8490 (t80) REVERT: C 102 ASN cc_start: 0.9581 (t0) cc_final: 0.9300 (m110) REVERT: C 129 MET cc_start: 0.8796 (mmm) cc_final: 0.8204 (tpp) REVERT: C 147 LYS cc_start: 0.9546 (mptt) cc_final: 0.9284 (mmtm) REVERT: C 168 TYR cc_start: 0.8183 (t80) cc_final: 0.7842 (t80) REVERT: C 181 ASP cc_start: 0.8843 (t0) cc_final: 0.8287 (p0) REVERT: C 203 PHE cc_start: 0.8851 (t80) cc_final: 0.8481 (t80) REVERT: J 19 ASP cc_start: 0.9155 (m-30) cc_final: 0.8854 (m-30) REVERT: J 63 ASP cc_start: 0.8724 (t0) cc_final: 0.8232 (t70) REVERT: J 97 ASP cc_start: 0.8996 (t70) cc_final: 0.8753 (t0) REVERT: M 12 HIS cc_start: 0.8926 (p90) cc_final: 0.8603 (p-80) REVERT: M 27 LYS cc_start: 0.9342 (tppt) cc_final: 0.9027 (tptt) REVERT: M 50 GLU cc_start: 0.9516 (pm20) cc_final: 0.9161 (tm-30) REVERT: S 17 LYS cc_start: 0.9603 (mptt) cc_final: 0.9373 (mttt) REVERT: S 66 MET cc_start: 0.9173 (mtp) cc_final: 0.8860 (mtp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1468 time to fit residues: 37.0267 Evaluate side-chains 118 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 50.0000 chunk 143 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.031543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.023057 restraints weight = 245645.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.023803 restraints weight = 131640.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.024180 restraints weight = 90211.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.024446 restraints weight = 73004.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.024593 restraints weight = 64846.793| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19802 Z= 0.177 Angle : 0.619 6.661 28949 Z= 0.317 Chirality : 0.036 0.260 3609 Planarity : 0.005 0.069 1995 Dihedral : 24.478 178.000 8374 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.25), residues: 1092 helix: -0.08 (0.22), residues: 506 sheet: -0.93 (0.38), residues: 166 loop : -1.23 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 10 TYR 0.014 0.002 TYR N 20 PHE 0.019 0.002 PHE C 37 TRP 0.010 0.002 TRP B 96 HIS 0.004 0.001 HIS S 83 Details of bonding type rmsd covalent geometry : bond 0.00344 (19801) covalent geometry : angle 0.61924 (28949) hydrogen bonds : bond 0.09998 ( 698) hydrogen bonds : angle 5.09549 ( 1576) metal coordination : bond 0.00224 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 THR cc_start: 0.4973 (p) cc_final: 0.4732 (p) REVERT: C 29 PHE cc_start: 0.9137 (t80) cc_final: 0.8334 (t80) REVERT: C 102 ASN cc_start: 0.9539 (t0) cc_final: 0.9292 (m110) REVERT: C 129 MET cc_start: 0.8793 (mmm) cc_final: 0.8190 (tpp) REVERT: C 147 LYS cc_start: 0.9527 (mptt) cc_final: 0.9285 (mmtm) REVERT: C 168 TYR cc_start: 0.8195 (t80) cc_final: 0.7968 (t80) REVERT: C 181 ASP cc_start: 0.8838 (t0) cc_final: 0.8325 (p0) REVERT: G 40 GLU cc_start: 0.8415 (pp20) cc_final: 0.8113 (mt-10) REVERT: J 19 ASP cc_start: 0.9171 (m-30) cc_final: 0.8864 (m-30) REVERT: J 63 ASP cc_start: 0.8752 (t0) cc_final: 0.8271 (t70) REVERT: J 97 ASP cc_start: 0.8984 (t70) cc_final: 0.8768 (t0) REVERT: M 12 HIS cc_start: 0.8732 (p90) cc_final: 0.8409 (p-80) REVERT: M 27 LYS cc_start: 0.9338 (tppt) cc_final: 0.9013 (tptt) REVERT: M 50 GLU cc_start: 0.9490 (pm20) cc_final: 0.9171 (tm-30) REVERT: S 66 MET cc_start: 0.9125 (mtp) cc_final: 0.8846 (mtp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1422 time to fit residues: 35.8277 Evaluate side-chains 121 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN N 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.022073 restraints weight = 266864.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.022671 restraints weight = 147353.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.023133 restraints weight = 106241.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.023360 restraints weight = 84536.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.023520 restraints weight = 74237.754| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19802 Z= 0.335 Angle : 0.790 8.318 28949 Z= 0.399 Chirality : 0.042 0.359 3609 Planarity : 0.006 0.071 1995 Dihedral : 24.852 179.699 8374 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 37.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.11 % Allowed : 0.98 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.25), residues: 1092 helix: -0.43 (0.21), residues: 509 sheet: -1.26 (0.37), residues: 161 loop : -1.34 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 3 TYR 0.016 0.002 TYR G 44 PHE 0.023 0.003 PHE C 37 TRP 0.018 0.002 TRP B 96 HIS 0.012 0.002 HIS S 57 Details of bonding type rmsd covalent geometry : bond 0.00636 (19801) covalent geometry : angle 0.79044 (28949) hydrogen bonds : bond 0.11959 ( 698) hydrogen bonds : angle 5.57524 ( 1576) metal coordination : bond 0.00458 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8616 (pp30) REVERT: B 208 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.7086 (ttp-170) REVERT: C 29 PHE cc_start: 0.9138 (t80) cc_final: 0.8747 (t80) REVERT: C 102 ASN cc_start: 0.9543 (t0) cc_final: 0.9298 (m110) REVERT: C 129 MET cc_start: 0.8702 (mmm) cc_final: 0.8162 (tpp) REVERT: C 168 TYR cc_start: 0.8156 (t80) cc_final: 0.7887 (t80) REVERT: C 181 ASP cc_start: 0.8854 (t0) cc_final: 0.8298 (p0) REVERT: G 40 GLU cc_start: 0.8394 (pp20) cc_final: 0.8087 (mt-10) REVERT: I 88 MET cc_start: 0.9485 (mmp) cc_final: 0.9195 (mmm) REVERT: J 63 ASP cc_start: 0.8695 (t0) cc_final: 0.8183 (t70) REVERT: J 97 ASP cc_start: 0.8986 (t70) cc_final: 0.8771 (t0) REVERT: M 27 LYS cc_start: 0.9342 (tppt) cc_final: 0.8967 (tppt) REVERT: S 66 MET cc_start: 0.9110 (mtp) cc_final: 0.8807 (mtp) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1453 time to fit residues: 34.1655 Evaluate side-chains 110 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 152 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.022936 restraints weight = 252610.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.023575 restraints weight = 137483.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.024097 restraints weight = 97804.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.024351 restraints weight = 78966.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.024454 restraints weight = 68571.882| |-----------------------------------------------------------------------------| r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19802 Z= 0.230 Angle : 0.685 7.714 28949 Z= 0.348 Chirality : 0.039 0.339 3609 Planarity : 0.005 0.070 1995 Dihedral : 24.718 177.801 8374 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1092 helix: -0.29 (0.22), residues: 507 sheet: -1.19 (0.38), residues: 161 loop : -1.25 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 3 TYR 0.019 0.002 TYR G 44 PHE 0.026 0.002 PHE C 37 TRP 0.014 0.002 TRP B 96 HIS 0.006 0.002 HIS S 57 Details of bonding type rmsd covalent geometry : bond 0.00442 (19801) covalent geometry : angle 0.68499 (28949) hydrogen bonds : bond 0.10427 ( 698) hydrogen bonds : angle 5.31110 ( 1576) metal coordination : bond 0.00255 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.4080 (mpp) cc_final: 0.3594 (mpp) REVERT: B 113 ARG cc_start: 0.9462 (mmm160) cc_final: 0.9008 (mtp180) REVERT: B 208 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7226 (ttp-170) REVERT: C 29 PHE cc_start: 0.9119 (t80) cc_final: 0.8570 (t80) REVERT: C 102 ASN cc_start: 0.9580 (t0) cc_final: 0.9274 (m110) REVERT: C 129 MET cc_start: 0.8718 (mmm) cc_final: 0.8156 (tpp) REVERT: C 168 TYR cc_start: 0.8148 (t80) cc_final: 0.7948 (t80) REVERT: C 181 ASP cc_start: 0.8852 (t0) cc_final: 0.8296 (p0) REVERT: G 40 GLU cc_start: 0.8359 (pp20) cc_final: 0.8087 (mt-10) REVERT: I 88 MET cc_start: 0.9497 (mmp) cc_final: 0.9232 (mmm) REVERT: I 118 LEU cc_start: 0.9340 (mm) cc_final: 0.9131 (mt) REVERT: J 19 ASP cc_start: 0.9135 (m-30) cc_final: 0.8801 (m-30) REVERT: J 63 ASP cc_start: 0.8718 (t0) cc_final: 0.8224 (t70) REVERT: J 97 ASP cc_start: 0.8976 (t70) cc_final: 0.8742 (t0) REVERT: M 12 HIS cc_start: 0.8695 (p90) cc_final: 0.8456 (p-80) REVERT: M 27 LYS cc_start: 0.9324 (tppt) cc_final: 0.8959 (tppt) REVERT: M 50 GLU cc_start: 0.9461 (pm20) cc_final: 0.9168 (tm-30) REVERT: M 81 MET cc_start: 0.9115 (mmp) cc_final: 0.8804 (mmp) REVERT: N 77 PHE cc_start: 0.9654 (m-80) cc_final: 0.9445 (m-80) REVERT: S 66 MET cc_start: 0.9145 (mtp) cc_final: 0.8885 (mtp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1419 time to fit residues: 34.0704 Evaluate side-chains 115 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 110 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 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 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.032203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.023397 restraints weight = 245342.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.024062 restraints weight = 131272.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.024512 restraints weight = 92910.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.024781 restraints weight = 73393.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.024873 restraints weight = 64781.432| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19802 Z= 0.152 Angle : 0.623 7.670 28949 Z= 0.318 Chirality : 0.037 0.230 3609 Planarity : 0.005 0.069 1995 Dihedral : 24.479 179.550 8374 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1092 helix: -0.16 (0.22), residues: 509 sheet: -1.04 (0.39), residues: 163 loop : -1.18 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 3 TYR 0.018 0.002 TYR N 20 PHE 0.025 0.001 PHE C 37 TRP 0.012 0.002 TRP C 201 HIS 0.004 0.001 HIS S 83 Details of bonding type rmsd covalent geometry : bond 0.00299 (19801) covalent geometry : angle 0.62316 (28949) hydrogen bonds : bond 0.09918 ( 698) hydrogen bonds : angle 5.13796 ( 1576) metal coordination : bond 0.00111 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.78 seconds wall clock time: 49 minutes 49.18 seconds (2989.18 seconds total)