Starting phenix.real_space_refine on Sat Sep 12 21:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afk_11768/09_2026/7afk_11768_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afk_11768/09_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_11768/09_2026/7afk_11768_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afk_11768/09_2026/7afk_11768_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afk_11768/09_2026/7afk_11768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afk_11768/09_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-2.2.1-6174/lib/python3.11/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: 3.02, per 1000 atoms: 0.16 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: 1.67 Conformation dependent library (CDL) restraints added in 375.0 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: 2.71 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: 3.70 Time building geometry restraints manager: 2.22 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=" N9 A 11105 " pdb=" C4 A 11105 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.41e+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=" N9 A 11339 " pdb=" C4 A 11339 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.34e+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 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27099 2.05 - 4.11: 1742 4.11 - 6.16: 89 6.16 - 8.21: 15 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 1.60e+00 3.91e-01 2.49e+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=" O5' C 11317 " pdb=" C5' C 11317 " pdb=" C4' C 11317 " ideal model delta sigma weight residual 109.40 113.10 -3.70 8.00e-01 1.56e+00 2.13e+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: 2870 0.077 - 0.154: 676 0.154 - 0.231: 52 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.180 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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= 0.637 Angle : 0.981 10.265 28949 Z= 0.788 Chirality : 0.063 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/Z covalent geometry : bond 0.00722 / 0.64 (19801) covalent geometry : angle 0.98119 / 0.79 (28949) hydrogen bonds : bond 0.27501 / 29.69 ( 698) hydrogen bonds : angle 9.72030 / 12.19 ( 1576) metal coordination : bond 0.15081 / 7.54 ( 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 : 0.395 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: symmetry clash REVERT: B 68 LEU cc_start: 0.8915 (tp) cc_final: 0.8530 (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: 0.7303 (mtt180) REVERT: B 161 LEU cc_start: 0.7981 (mt) cc_final: 0.6812 (mt) REVERT: B 181 ILE cc_start: 0.8233 (mt) cc_final: 0.7916 (tp) REVERT: C 102 ASN cc_start: 0.9455 (t0) cc_final: 0.9197 (m110) REVERT: C 129 MET cc_start: 0.8870 (mmm) cc_final: 0.8226 (tpp) REVERT: C 150 LYS cc_start: 0.8551 (tttm) cc_final: 0.8062 (tptp) REVERT: C 181 ASP cc_start: 0.9054 (t0) cc_final: 0.8369 (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: 0.7206 (p) REVERT: I 32 GLN cc_start: 0.8757 (mm110) cc_final: 0.8549 (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: 0.8818 (pm20) REVERT: I 112 GLU cc_start: 0.8217 (tt0) cc_final: 0.7756 (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: 0.8946 (tt) REVERT: J 63 ASP cc_start: 0.8579 (t0) cc_final: 0.7662 (t0) REVERT: J 65 TYR cc_start: 0.8477 (m-80) cc_final: 0.8112 (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: 0.8921 (pttp) REVERT: M 50 GLU cc_start: 0.9519 (pm20) cc_final: 0.9142 (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: 0.8357 (mt) REVERT: N 86 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8749 (mt-10) REVERT: N 101 TRP cc_start: 0.8402 (p90) cc_final: 0.6029 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1592 time to fit residues: 55.8424 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 : 0.383 ------------------------------------------------------------------------------- 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: 30.0000 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: 7.9990 chunk 149 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 227 GLN G 122 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.031477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.022777 restraints weight = 254958.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.023507 restraints weight = 140401.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.023899 restraints weight = 97547.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.024191 restraints weight = 79278.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.024317 restraints weight = 69667.369| |-----------------------------------------------------------------------------| r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19802 Z= 0.216 Angle : 0.715 12.694 28949 Z= 0.388 Chirality : 0.046 0.291 3609 Planarity : 0.007 0.083 1995 Dihedral : 24.883 178.740 8374 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 30.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1092 helix: -0.72 (0.22), residues: 493 sheet: -1.96 (0.36), residues: 156 loop : -1.97 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 92 TYR 0.014 0.002 TYR J 65 PHE 0.027 0.003 PHE G 151 TRP 0.023 0.003 TRP B 96 HIS 0.006 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.22 (19801) covalent geometry : angle 0.71539 / 0.39 (28949) hydrogen bonds : bond 0.15690 / 16.61 ( 698) hydrogen bonds : angle 6.10572 / 8.10 ( 1576) metal coordination : bond 0.02044 / 1.02 ( 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 193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.354 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 94 HIS cc_start: 0.9078 (t70) cc_final: 0.8775 (t70) REVERT: B 117 LEU cc_start: 0.8571 (mt) cc_final: 0.7898 (mt) REVERT: C 41 GLN cc_start: 0.9459 (pp30) cc_final: 0.9248 (pp30) REVERT: C 102 ASN cc_start: 0.9606 (t0) cc_final: 0.9156 (m110) REVERT: C 129 MET cc_start: 0.8819 (mmm) cc_final: 0.8218 (tpp) REVERT: C 142 MET cc_start: 0.9095 (tpp) cc_final: 0.8768 (tpt) REVERT: C 181 ASP cc_start: 0.8904 (t0) cc_final: 0.8169 (p0) REVERT: C 203 PHE cc_start: 0.9056 (t80) cc_final: 0.8645 (t80) REVERT: I 110 GLN cc_start: 0.9535 (pt0) cc_final: 0.8894 (pm20) REVERT: J 19 ASP cc_start: 0.9203 (m-30) cc_final: 0.8894 (m-30) REVERT: J 46 LYS cc_start: 0.9011 (mptt) cc_final: 0.8745 (mmtm) REVERT: J 63 ASP cc_start: 0.7999 (t0) cc_final: 0.7680 (t0) REVERT: M 12 HIS cc_start: 0.8772 (p90) cc_final: 0.8374 (p-80) REVERT: M 27 LYS cc_start: 0.9340 (tppt) cc_final: 0.8781 (tppt) REVERT: M 31 LYS cc_start: 0.9245 (pttm) cc_final: 0.9027 (pttp) REVERT: M 50 GLU cc_start: 0.9485 (pm20) cc_final: 0.9130 (tm-30) REVERT: M 81 MET cc_start: 0.9108 (mtt) cc_final: 0.8823 (mtt) REVERT: N 86 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9131 (mt-10) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1587 time to fit residues: 45.7584 Evaluate side-chains 130 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 20.0000 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS C 140 ASN 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 = 0.2646 r_free = 0.2646 target = 0.030711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.022392 restraints weight = 254942.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.023121 restraints weight = 138717.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.023502 restraints weight = 96363.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.023820 restraints weight = 78743.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.023949 restraints weight = 68260.653| |-----------------------------------------------------------------------------| r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19802 Z= 0.238 Angle : 0.675 10.750 28949 Z= 0.370 Chirality : 0.044 0.317 3609 Planarity : 0.006 0.084 1995 Dihedral : 24.799 179.529 8374 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % 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: -1.98 (0.24), residues: 1092 helix: -0.53 (0.22), residues: 488 sheet: -1.70 (0.37), residues: 156 loop : -1.96 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 63 TYR 0.039 0.003 TYR G 44 PHE 0.016 0.002 PHE B 90 TRP 0.011 0.002 TRP S 34 HIS 0.006 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.24 (19801) covalent geometry : angle 0.67462 / 0.37 (28949) hydrogen bonds : bond 0.13655 / 14.37 ( 698) hydrogen bonds : angle 5.95686 / 7.85 ( 1576) metal coordination : bond 0.00596 / 0.30 ( 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 179 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.370 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 94 HIS cc_start: 0.8993 (t70) cc_final: 0.8685 (t70) REVERT: B 113 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.7844 (mtm110) REVERT: B 186 ILE cc_start: 0.4420 (tp) cc_final: 0.4104 (tp) REVERT: C 41 GLN cc_start: 0.9475 (pp30) cc_final: 0.9243 (pp30) REVERT: C 102 ASN cc_start: 0.9611 (t0) cc_final: 0.9145 (m110) REVERT: C 129 MET cc_start: 0.8842 (mmm) cc_final: 0.8249 (tpp) REVERT: C 142 MET cc_start: 0.9140 (tpp) cc_final: 0.8891 (tpt) REVERT: C 150 LYS cc_start: 0.8564 (tttm) cc_final: 0.8082 (tptp) REVERT: C 181 ASP cc_start: 0.8931 (t0) cc_final: 0.8281 (p0) REVERT: G 78 ARG cc_start: 0.7777 (mpp-170) cc_final: 0.7227 (mmp-170) REVERT: I 61 LEU cc_start: 0.9843 (pt) cc_final: 0.9632 (mp) REVERT: I 110 GLN cc_start: 0.9455 (pt0) cc_final: 0.8876 (pm20) REVERT: J 19 ASP cc_start: 0.9226 (m-30) cc_final: 0.8942 (m-30) REVERT: J 63 ASP cc_start: 0.8555 (t0) cc_final: 0.7898 (t0) REVERT: J 65 TYR cc_start: 0.8783 (m-80) cc_final: 0.8380 (m-80) REVERT: J 88 MET cc_start: 0.9372 (mtm) cc_final: 0.9154 (mtp) REVERT: M 27 LYS cc_start: 0.9375 (tppt) cc_final: 0.9006 (tppt) REVERT: M 50 GLU cc_start: 0.9557 (pm20) cc_final: 0.9131 (tm-30) REVERT: M 69 LEU cc_start: 0.9563 (tp) cc_final: 0.9363 (tp) REVERT: M 81 MET cc_start: 0.9148 (mtt) cc_final: 0.8888 (mtt) REVERT: N 20 TYR cc_start: 0.9100 (m-10) cc_final: 0.8877 (m-10) REVERT: N 86 GLU cc_start: 0.9579 (mt-10) cc_final: 0.9318 (mt-10) REVERT: S 66 MET cc_start: 0.9453 (mtp) cc_final: 0.9174 (mtp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1552 time to fit residues: 41.2756 Evaluate side-chains 128 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 30.0000 chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 58 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** 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 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.030526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.022090 restraints weight = 257859.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.022781 restraints weight = 140579.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.023200 restraints weight = 97737.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.023459 restraints weight = 79490.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.023615 restraints weight = 69402.062| |-----------------------------------------------------------------------------| r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19802 Z= 0.234 Angle : 0.665 9.790 28949 Z= 0.364 Chirality : 0.044 0.309 3609 Planarity : 0.006 0.082 1995 Dihedral : 24.774 179.703 8374 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 32.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -1.91 (0.24), residues: 1092 helix: -0.59 (0.22), residues: 496 sheet: -1.38 (0.38), residues: 156 loop : -1.90 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 108 TYR 0.023 0.002 TYR G 44 PHE 0.022 0.002 PHE B 184 TRP 0.012 0.002 TRP G 103 HIS 0.012 0.002 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.23 (19801) covalent geometry : angle 0.66548 / 0.36 (28949) hydrogen bonds : bond 0.13338 / 14.10 ( 698) hydrogen bonds : angle 5.80616 / 7.63 ( 1576) metal coordination : bond 0.00547 / 0.27 ( 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 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.448 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8829 (t70) cc_final: 0.8406 (t70) REVERT: C 29 PHE cc_start: 0.8924 (t80) cc_final: 0.8169 (t80) REVERT: C 41 GLN cc_start: 0.9486 (pp30) cc_final: 0.9236 (pp30) REVERT: C 102 ASN cc_start: 0.9632 (t0) cc_final: 0.9200 (m110) REVERT: C 129 MET cc_start: 0.8873 (mmm) cc_final: 0.8326 (tpp) REVERT: C 142 MET cc_start: 0.9149 (tpp) cc_final: 0.8851 (tpt) REVERT: C 168 TYR cc_start: 0.8129 (t80) cc_final: 0.7735 (t80) REVERT: C 181 ASP cc_start: 0.8939 (t0) cc_final: 0.8338 (p0) REVERT: G 15 ASP cc_start: 0.7815 (t0) cc_final: 0.7610 (t70) REVERT: G 78 ARG cc_start: 0.7721 (mpp-170) cc_final: 0.7387 (mtp85) REVERT: I 118 LEU cc_start: 0.9472 (mm) cc_final: 0.9219 (mt) REVERT: I 130 ARG cc_start: 0.7962 (mtt-85) cc_final: 0.7561 (mtm-85) REVERT: J 19 ASP cc_start: 0.9248 (m-30) cc_final: 0.8997 (m-30) REVERT: J 63 ASP cc_start: 0.8598 (t0) cc_final: 0.8177 (t70) REVERT: J 88 MET cc_start: 0.9359 (mtm) cc_final: 0.9118 (mtp) REVERT: M 27 LYS cc_start: 0.9336 (tppt) cc_final: 0.8981 (tppt) REVERT: M 50 GLU cc_start: 0.9545 (pm20) cc_final: 0.9136 (tm-30) REVERT: M 81 MET cc_start: 0.9163 (mtt) cc_final: 0.8916 (mtt) REVERT: N 20 TYR cc_start: 0.9141 (m-10) cc_final: 0.8904 (m-10) REVERT: N 82 ILE cc_start: 0.9161 (mt) cc_final: 0.8820 (mt) REVERT: S 44 MET cc_start: 0.9337 (tpt) cc_final: 0.9130 (tpp) REVERT: S 66 MET cc_start: 0.9428 (mtp) cc_final: 0.9163 (mtp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1551 time to fit residues: 38.3644 Evaluate side-chains 122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.031489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.023167 restraints weight = 250040.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.023875 restraints weight = 134570.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.024353 restraints weight = 92895.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.024610 restraints weight = 75064.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024776 restraints weight = 66018.501| |-----------------------------------------------------------------------------| r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19802 Z= 0.176 Angle : 0.616 10.846 28949 Z= 0.339 Chirality : 0.040 0.297 3609 Planarity : 0.006 0.066 1995 Dihedral : 24.680 179.542 8374 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % 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: -1.68 (0.24), residues: 1092 helix: -0.46 (0.21), residues: 503 sheet: -1.22 (0.37), residues: 166 loop : -1.73 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 108 TYR 0.019 0.002 TYR G 44 PHE 0.020 0.002 PHE B 50 TRP 0.012 0.002 TRP N 101 HIS 0.006 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.18 (19801) covalent geometry : angle 0.61599 / 0.34 (28949) hydrogen bonds : bond 0.12413 / 13.14 ( 698) hydrogen bonds : angle 5.61681 / 7.34 ( 1576) metal coordination : bond 0.00572 / 0.29 ( 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 175 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.477 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 94 HIS cc_start: 0.8855 (t70) cc_final: 0.8394 (t70) REVERT: B 113 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8025 (mtm110) REVERT: C 102 ASN cc_start: 0.9603 (t0) cc_final: 0.9246 (m110) REVERT: C 129 MET cc_start: 0.8794 (mmm) cc_final: 0.8207 (tpp) REVERT: C 142 MET cc_start: 0.9216 (tpp) cc_final: 0.8947 (tpt) REVERT: C 168 TYR cc_start: 0.8077 (t80) cc_final: 0.7646 (t80) REVERT: C 181 ASP cc_start: 0.8901 (t0) cc_final: 0.8295 (p0) REVERT: G 15 ASP cc_start: 0.7877 (t0) cc_final: 0.7670 (t70) REVERT: G 78 ARG cc_start: 0.7638 (mpp-170) cc_final: 0.7160 (mmm160) REVERT: I 118 LEU cc_start: 0.9457 (mm) cc_final: 0.9234 (mt) REVERT: I 130 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7725 (mtm-85) REVERT: J 19 ASP cc_start: 0.9297 (m-30) cc_final: 0.8996 (m-30) REVERT: J 63 ASP cc_start: 0.8490 (t0) cc_final: 0.7939 (t70) REVERT: M 12 HIS cc_start: 0.8904 (p90) cc_final: 0.8536 (p-80) REVERT: M 27 LYS cc_start: 0.9339 (tppt) cc_final: 0.8969 (tppt) REVERT: M 50 GLU cc_start: 0.9565 (pm20) cc_final: 0.9182 (tm-30) REVERT: M 75 MET cc_start: 0.9509 (ptp) cc_final: 0.9099 (mmt) REVERT: M 81 MET cc_start: 0.9165 (mtt) cc_final: 0.8883 (mtt) REVERT: S 44 MET cc_start: 0.9344 (tpt) cc_final: 0.9139 (tpp) REVERT: S 66 MET cc_start: 0.9360 (mtp) cc_final: 0.9146 (mtp) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1733 time to fit residues: 43.8666 Evaluate side-chains 122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 0.0980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.032419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.023842 restraints weight = 242146.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024588 restraints weight = 130503.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.025073 restraints weight = 89901.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.025377 restraints weight = 72070.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.025505 restraints weight = 62769.851| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19802 Z= 0.138 Angle : 0.604 10.924 28949 Z= 0.332 Chirality : 0.039 0.262 3609 Planarity : 0.006 0.094 1995 Dihedral : 24.517 179.422 8374 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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 (0.24), residues: 1092 helix: -0.28 (0.22), residues: 506 sheet: -1.13 (0.37), residues: 167 loop : -1.59 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG J 9 TYR 0.012 0.001 TYR G 44 PHE 0.017 0.002 PHE B 50 TRP 0.022 0.002 TRP N 101 HIS 0.009 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (19801) covalent geometry : angle 0.60438 / 0.33 (28949) hydrogen bonds : bond 0.11813 / 12.51 ( 698) hydrogen bonds : angle 5.50067 / 7.15 ( 1576) metal coordination : bond 0.00034 / 0.02 ( 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 177 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.598 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: 0.8831 (t70) cc_final: 0.8341 (t70) REVERT: C 102 ASN cc_start: 0.9628 (t0) cc_final: 0.9266 (m110) REVERT: C 129 MET cc_start: 0.8780 (mmm) cc_final: 0.8157 (tpp) REVERT: C 168 TYR cc_start: 0.8000 (t80) cc_final: 0.7536 (t80) REVERT: C 181 ASP cc_start: 0.8896 (t0) cc_final: 0.8238 (p0) REVERT: C 203 PHE cc_start: 0.8853 (t80) cc_final: 0.8402 (t80) REVERT: I 27 LYS cc_start: 0.8935 (pttm) cc_final: 0.8731 (mmtt) REVERT: J 19 ASP cc_start: 0.9271 (m-30) cc_final: 0.8982 (m-30) REVERT: J 63 ASP cc_start: 0.8604 (t0) cc_final: 0.7943 (t70) REVERT: J 65 TYR cc_start: 0.8874 (m-80) cc_final: 0.8172 (m-80) REVERT: M 12 HIS cc_start: 0.8847 (p90) cc_final: 0.8493 (p-80) REVERT: M 27 LYS cc_start: 0.9357 (tppt) cc_final: 0.8806 (tppt) REVERT: M 31 LYS cc_start: 0.9229 (pttm) cc_final: 0.9013 (pttp) REVERT: M 50 GLU cc_start: 0.9550 (pm20) cc_final: 0.9079 (tm-30) REVERT: M 81 MET cc_start: 0.9128 (mtt) cc_final: 0.8822 (mtt) REVERT: S 17 LYS cc_start: 0.9583 (mptt) cc_final: 0.9378 (mttt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1678 time to fit residues: 43.7104 Evaluate side-chains 119 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 40.0000 chunk 94 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 120 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.031111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.022638 restraints weight = 250954.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.023338 restraints weight = 137138.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.023735 restraints weight = 95598.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.023940 restraints weight = 77735.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.024127 restraints weight = 70389.745| |-----------------------------------------------------------------------------| r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19802 Z= 0.219 Angle : 0.657 8.568 28949 Z= 0.353 Chirality : 0.042 0.284 3609 Planarity : 0.007 0.088 1995 Dihedral : 24.534 179.663 8374 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -1.49 (0.24), residues: 1092 helix: -0.35 (0.22), residues: 503 sheet: -1.11 (0.36), residues: 168 loop : -1.59 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 3 TYR 0.013 0.002 TYR N 20 PHE 0.022 0.003 PHE B 126 TRP 0.013 0.002 TRP N 101 HIS 0.009 0.002 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.22 (19801) covalent geometry : angle 0.65731 / 0.35 (28949) hydrogen bonds : bond 0.11988 / 12.64 ( 698) hydrogen bonds : angle 5.56340 / 7.23 ( 1576) metal coordination : bond 0.00613 / 0.31 ( 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 161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.416 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: 0.8515 (mtm-85) cc_final: 0.8091 (mtm180) REVERT: C 102 ASN cc_start: 0.9621 (t0) cc_final: 0.9284 (m110) REVERT: C 129 MET cc_start: 0.8853 (mmm) cc_final: 0.8267 (tpp) REVERT: C 134 MET cc_start: 0.8677 (ptm) cc_final: 0.8471 (ptm) REVERT: C 168 TYR cc_start: 0.8124 (t80) cc_final: 0.7790 (t80) REVERT: C 181 ASP cc_start: 0.8927 (t0) cc_final: 0.8320 (p0) REVERT: G 15 ASP cc_start: 0.7825 (t0) cc_final: 0.7612 (t0) REVERT: I 42 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9006 (tp30) REVERT: J 19 ASP cc_start: 0.9220 (m-30) cc_final: 0.8894 (m-30) REVERT: J 63 ASP cc_start: 0.8587 (t0) cc_final: 0.8008 (t70) REVERT: M 12 HIS cc_start: 0.8881 (p90) cc_final: 0.8633 (p-80) REVERT: M 27 LYS cc_start: 0.9351 (tppt) cc_final: 0.8980 (tppt) REVERT: M 50 GLU cc_start: 0.9559 (pm20) cc_final: 0.9209 (tm-30) REVERT: M 81 MET cc_start: 0.9180 (mtt) cc_final: 0.8897 (mtt) REVERT: S 66 MET cc_start: 0.9236 (mtp) cc_final: 0.8983 (mtp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1600 time to fit residues: 38.8126 Evaluate side-chains 119 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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: 7.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 63 optimal weight: 30.0000 chunk 143 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.031826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.023065 restraints weight = 246616.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.023815 restraints weight = 133961.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.024194 restraints weight = 92431.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.024540 restraints weight = 75749.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.024672 restraints weight = 65997.942| |-----------------------------------------------------------------------------| r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19802 Z= 0.141 Angle : 0.590 8.295 28949 Z= 0.324 Chirality : 0.039 0.255 3609 Planarity : 0.006 0.069 1995 Dihedral : 24.451 179.398 8374 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -1.29 (0.24), residues: 1092 helix: -0.26 (0.22), residues: 501 sheet: -1.07 (0.37), residues: 167 loop : -1.35 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.009 0.001 TYR B 213 PHE 0.021 0.002 PHE B 91 TRP 0.013 0.002 TRP C 201 HIS 0.003 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (19801) covalent geometry : angle 0.59034 / 0.32 (28949) hydrogen bonds : bond 0.11589 / 12.27 ( 698) hydrogen bonds : angle 5.35920 / 6.98 ( 1576) metal coordination : bond 0.00371 / 0.19 ( 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 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.445 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 94 HIS cc_start: 0.8693 (t70) cc_final: 0.8203 (t70) REVERT: C 102 ASN cc_start: 0.9629 (t0) cc_final: 0.9301 (m110) REVERT: C 129 MET cc_start: 0.8726 (mmm) cc_final: 0.8105 (tpp) REVERT: C 168 TYR cc_start: 0.8092 (t80) cc_final: 0.7700 (t80) REVERT: C 181 ASP cc_start: 0.8893 (t0) cc_final: 0.8324 (p0) REVERT: G 15 ASP cc_start: 0.7808 (t0) cc_final: 0.7573 (t0) REVERT: G 78 ARG cc_start: 0.7552 (mpp-170) cc_final: 0.7054 (mmm160) REVERT: I 42 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9034 (tp30) REVERT: J 19 ASP cc_start: 0.9270 (m-30) cc_final: 0.8976 (m-30) REVERT: J 63 ASP cc_start: 0.8651 (t0) cc_final: 0.8013 (t70) REVERT: J 65 TYR cc_start: 0.8766 (m-80) cc_final: 0.8142 (m-80) REVERT: M 12 HIS cc_start: 0.8896 (p90) cc_final: 0.8546 (p-80) REVERT: M 27 LYS cc_start: 0.9352 (tppt) cc_final: 0.8831 (tppt) REVERT: M 31 LYS cc_start: 0.9243 (pttm) cc_final: 0.9038 (pttp) REVERT: M 50 GLU cc_start: 0.9582 (pm20) cc_final: 0.9100 (tm-30) REVERT: M 75 MET cc_start: 0.9413 (ptp) cc_final: 0.9153 (tmm) REVERT: M 81 MET cc_start: 0.9120 (mtt) cc_final: 0.8825 (mtt) REVERT: S 66 MET cc_start: 0.9217 (mtp) cc_final: 0.8941 (mtp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1524 time to fit residues: 38.4248 Evaluate side-chains 124 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 30.0000 chunk 5 optimal weight: 30.0000 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 0.0670 chunk 46 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.031513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.022819 restraints weight = 248667.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.023596 restraints weight = 135937.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.023963 restraints weight = 93285.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.024279 restraints weight = 75967.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.024415 restraints weight = 66384.867| |-----------------------------------------------------------------------------| r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19802 Z= 0.167 Angle : 0.614 9.981 28949 Z= 0.334 Chirality : 0.040 0.349 3609 Planarity : 0.006 0.123 1995 Dihedral : 24.388 179.774 8374 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.32 (0.24), residues: 1092 helix: -0.32 (0.22), residues: 511 sheet: -1.03 (0.37), residues: 167 loop : -1.34 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 10 TYR 0.018 0.002 TYR N 20 PHE 0.024 0.002 PHE B 50 TRP 0.012 0.002 TRP B 104 HIS 0.005 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (19801) covalent geometry : angle 0.61396 / 0.33 (28949) hydrogen bonds : bond 0.11382 / 12.05 ( 698) hydrogen bonds : angle 5.41191 / 7.02 ( 1576) metal coordination : bond 0.00490 / 0.25 ( 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 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 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: B 94 HIS cc_start: 0.8695 (t70) cc_final: 0.8178 (t70) REVERT: C 102 ASN cc_start: 0.9630 (t0) cc_final: 0.9300 (m110) REVERT: C 129 MET cc_start: 0.8825 (mmm) cc_final: 0.8246 (tpp) REVERT: C 134 MET cc_start: 0.8741 (ptm) cc_final: 0.8535 (ptm) REVERT: C 168 TYR cc_start: 0.8103 (t80) cc_final: 0.7718 (t80) REVERT: C 181 ASP cc_start: 0.8895 (t0) cc_final: 0.8359 (p0) REVERT: G 78 ARG cc_start: 0.7623 (mpp-170) cc_final: 0.7105 (mmm160) REVERT: J 19 ASP cc_start: 0.9257 (m-30) cc_final: 0.8962 (m-30) REVERT: J 63 ASP cc_start: 0.8603 (t0) cc_final: 0.8051 (t70) REVERT: J 65 TYR cc_start: 0.8792 (m-80) cc_final: 0.8350 (m-80) REVERT: M 12 HIS cc_start: 0.8921 (p90) cc_final: 0.8574 (p-80) REVERT: M 27 LYS cc_start: 0.9344 (tppt) cc_final: 0.8987 (tppt) REVERT: M 50 GLU cc_start: 0.9579 (pm20) cc_final: 0.9103 (tm-30) REVERT: M 72 GLU cc_start: 0.9630 (tp30) cc_final: 0.9378 (tp30) REVERT: M 81 MET cc_start: 0.9131 (mtt) cc_final: 0.8839 (mtt) REVERT: N 89 MET cc_start: 0.9160 (mmp) cc_final: 0.8452 (mmp) REVERT: S 66 MET cc_start: 0.9208 (mtp) cc_final: 0.8960 (mtp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1475 time to fit residues: 35.3096 Evaluate side-chains 119 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.0980 chunk 146 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 133 optimal weight: 0.0270 chunk 65 optimal weight: 0.0870 chunk 36 optimal weight: 30.0000 chunk 9 optimal weight: 40.0000 chunk 62 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.024173 restraints weight = 237409.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.024955 restraints weight = 129199.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.025455 restraints weight = 89715.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025785 restraints weight = 71668.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025923 restraints weight = 62442.616| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19802 Z= 0.127 Angle : 0.611 15.960 28949 Z= 0.334 Chirality : 0.039 0.338 3609 Planarity : 0.006 0.075 1995 Dihedral : 24.220 179.464 8374 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % 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: -1.22 (0.24), residues: 1092 helix: -0.34 (0.22), residues: 510 sheet: -0.75 (0.39), residues: 155 loop : -1.25 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 108 TYR 0.010 0.001 TYR N 20 PHE 0.024 0.002 PHE B 50 TRP 0.017 0.002 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (19801) covalent geometry : angle 0.61057 / 0.33 (28949) hydrogen bonds : bond 0.11512 / 12.39 ( 698) hydrogen bonds : angle 5.17067 / 6.67 ( 1576) metal coordination : bond 0.00130 / 0.06 ( 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 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.496 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: B 94 HIS cc_start: 0.8735 (t70) cc_final: 0.8276 (t70) REVERT: B 113 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7983 (mtm110) REVERT: C 102 ASN cc_start: 0.9612 (t0) cc_final: 0.9283 (m110) REVERT: C 129 MET cc_start: 0.8605 (mmm) cc_final: 0.7974 (tpp) REVERT: C 134 MET cc_start: 0.8651 (ptm) cc_final: 0.8416 (ptm) REVERT: C 142 MET cc_start: 0.8483 (mmm) cc_final: 0.7677 (tpt) REVERT: C 168 TYR cc_start: 0.8166 (t80) cc_final: 0.7827 (t80) REVERT: C 170 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8735 (tm-30) REVERT: G 78 ARG cc_start: 0.7495 (mpp-170) cc_final: 0.6991 (mmm160) REVERT: I 110 GLN cc_start: 0.9458 (pt0) cc_final: 0.8926 (pm20) REVERT: J 63 ASP cc_start: 0.8685 (t0) cc_final: 0.8025 (t70) REVERT: J 65 TYR cc_start: 0.8768 (m-80) cc_final: 0.8201 (m-80) REVERT: J 88 MET cc_start: 0.9539 (mpp) cc_final: 0.9233 (mpp) REVERT: J 97 ASP cc_start: 0.9069 (t0) cc_final: 0.8816 (t0) REVERT: M 12 HIS cc_start: 0.8925 (p90) cc_final: 0.8630 (p-80) REVERT: M 27 LYS cc_start: 0.9328 (tppt) cc_final: 0.8801 (tppt) REVERT: M 50 GLU cc_start: 0.9578 (pm20) cc_final: 0.9096 (tp30) REVERT: S 66 MET cc_start: 0.9172 (mtp) cc_final: 0.8883 (mtp) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1526 time to fit residues: 41.7284 Evaluate side-chains 125 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN C 139 GLN I 50 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.033093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.024129 restraints weight = 237264.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.024865 restraints weight = 130826.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.025343 restraints weight = 91424.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025650 restraints weight = 73270.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.025839 restraints weight = 64515.084| |-----------------------------------------------------------------------------| r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19802 Z= 0.123 Angle : 0.575 7.726 28949 Z= 0.317 Chirality : 0.037 0.299 3609 Planarity : 0.006 0.099 1995 Dihedral : 24.125 179.767 8374 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % 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: -1.14 (0.24), residues: 1092 helix: -0.29 (0.22), residues: 507 sheet: -0.47 (0.40), residues: 155 loop : -1.29 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 124 TYR 0.019 0.001 TYR N 20 PHE 0.023 0.002 PHE B 50 TRP 0.012 0.001 TRP C 18 HIS 0.004 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (19801) covalent geometry : angle 0.57528 / 0.32 (28949) hydrogen bonds : bond 0.10991 / 11.80 ( 698) hydrogen bonds : angle 5.18374 / 6.74 ( 1576) metal coordination : bond 0.00134 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.74 seconds wall clock time: 51 minutes 19.65 seconds (3079.65 seconds total)