Starting phenix.real_space_refine on Fri Oct 23 23:47:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u4j_8506/10_2026/5u4j_8506_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u4j_8506/10_2026/5u4j_8506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u4j_8506/10_2026/5u4j_8506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u4j_8506/10_2026/5u4j_8506.map" model { file = "/net/cci-nas-00/data/ceres_data/5u4j_8506/10_2026/5u4j_8506_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u4j_8506/10_2026/5u4j_8506_neut.cif" } resolution = 3.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 339 5.49 5 S 15 5.16 5 C 5794 2.51 5 N 2109 2.21 5 O 3103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 6591 Classifications: {'RNA': 306, 'RNAv2': 1} Modifications used: {'rna2p': 1, 'rna2p_pur': 23, 'rna2p_pyr': 19, 'rna3p': 7, 'rna3p_pur': 144, 'rna3p_pyr': 113} Link IDs: {'rna2p': 43, 'rna3p': 263} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 233 Classifications: {'RNA': 9, 'RNAv2': 2} Modifications used: {'rna2p_pur': 2, 'rna3p': 2, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "c" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 169 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "d" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 523 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "e" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "z" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 315 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna3p': 14} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "v" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1054 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "w" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 2.35, per 1000 atoms: 0.21 Number of scatterers: 11360 At special positions: 0 Unit cell: (102.598, 114.528, 102.598, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 339 15.00 O 3103 8.00 N 2109 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 284.7 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 27.3% alpha, 30.2% beta 97 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.983A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 Processing helix chain 'd' and resid 49 through 65 removed outlier: 3.722A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL d 61 " --> pdb=" O GLU d 57 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG d 62 " --> pdb=" O LYS d 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE d 64 " --> pdb=" O LYS d 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.665A pdb=" N GLN e 61 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 119 removed outlier: 4.027A pdb=" N VAL e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL e 117 " --> pdb=" O ALA e 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 removed outlier: 4.108A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.803A pdb=" N ARG l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 139 through 160 removed outlier: 3.544A pdb=" N ARG v 159 " --> pdb=" O TRP v 155 " (cutoff:3.500A) Processing helix chain 'v' and resid 187 through 192 removed outlier: 3.864A pdb=" N TRP v 191 " --> pdb=" O TYR v 187 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU v 192 " --> pdb=" O ALA v 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 187 through 192' Processing helix chain 'v' and resid 297 through 316 Processing helix chain 'w' and resid 14 through 21 Processing helix chain 'w' and resid 22 through 26 removed outlier: 3.828A pdb=" N ARG w 26 " --> pdb=" O PRO w 23 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 151 through 155 Processing sheet with id=AA2, first strand: chain 'e' and resid 12 through 24 removed outlier: 5.216A pdb=" N GLU e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY e 40 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 85 through 89 removed outlier: 6.748A pdb=" N ILE e 106 " --> pdb=" O ALA e 125 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA e 127 " --> pdb=" O ILE e 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'l' and resid 30 through 40 removed outlier: 6.665A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'v' and resid 164 through 170 removed outlier: 5.429A pdb=" N ILE v 165 " --> pdb=" O LYS v 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS v 182 " --> pdb=" O ILE v 165 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS v 177 " --> pdb=" O ALA v 134 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY v 135 " --> pdb=" O PHE v 217 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE v 217 " --> pdb=" O GLY v 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY v 197 " --> pdb=" O ALA v 220 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL v 198 " --> pdb=" O GLN v 322 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG v 324 " --> pdb=" O VAL v 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'v' and resid 164 through 170 removed outlier: 5.429A pdb=" N ILE v 165 " --> pdb=" O LYS v 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS v 182 " --> pdb=" O ILE v 165 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS v 177 " --> pdb=" O ALA v 134 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY v 135 " --> pdb=" O PHE v 217 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE v 217 " --> pdb=" O GLY v 135 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 240 hydrogen bonds 396 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2289 1.34 - 1.45: 4498 1.45 - 1.57: 4797 1.57 - 1.69: 670 1.69 - 1.81: 24 Bond restraints: 12278 Sorted by residual: bond pdb=" P G7M a 527 " pdb=" OP1 G7M a 527 " ideal model delta sigma weight residual 1.525 1.649 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C4 PSU A1917 " pdb=" C5 PSU A1917 " ideal model delta sigma weight residual 1.390 1.498 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C4 PSU a 516 " pdb=" C5 PSU a 516 " ideal model delta sigma weight residual 1.390 1.497 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 PSU A1911 " pdb=" C5 PSU A1911 " ideal model delta sigma weight residual 1.390 1.494 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O3' C a 526 " pdb=" P G7M a 527 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.48e+01 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 18029 3.77 - 7.55: 124 7.55 - 11.32: 32 11.32 - 15.09: 3 15.09 - 18.87: 1 Bond angle restraints: 18189 Sorted by residual: angle pdb=" O3' G7M a 527 " pdb=" P C a 528 " pdb=" O5' C a 528 " ideal model delta sigma weight residual 104.00 122.87 -18.87 1.90e+00 2.77e-01 9.86e+01 angle pdb=" N LYS w 8 " pdb=" CA LYS w 8 " pdb=" C LYS w 8 " ideal model delta sigma weight residual 110.97 102.56 8.41 1.09e+00 8.42e-01 5.95e+01 angle pdb=" C LYS w 8 " pdb=" CA LYS w 8 " pdb=" CB LYS w 8 " ideal model delta sigma weight residual 110.96 121.87 -10.91 1.54e+00 4.22e-01 5.02e+01 angle pdb=" C3' C a 526 " pdb=" O3' C a 526 " pdb=" P G7M a 527 " ideal model delta sigma weight residual 119.70 111.48 8.22 1.20e+00 6.94e-01 4.69e+01 angle pdb=" O3' G a1064 " pdb=" C3' G a1064 " pdb=" C2' G a1064 " ideal model delta sigma weight residual 109.50 121.44 -11.94 2.20e+00 2.07e-01 2.95e+01 ... (remaining 18184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6947 35.82 - 71.64: 824 71.64 - 107.47: 108 107.47 - 143.29: 4 143.29 - 179.11: 5 Dihedral angle restraints: 7888 sinusoidal: 6418 harmonic: 1470 Sorted by residual: dihedral pdb=" C5' A a 560 " pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" O3' A a 560 " ideal model delta sinusoidal sigma weight residual 147.00 82.18 64.82 1 8.00e+00 1.56e-02 8.62e+01 dihedral pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" C2' A a 560 " pdb=" C1' A a 560 " ideal model delta sinusoidal sigma weight residual -35.00 26.81 -61.81 1 8.00e+00 1.56e-02 7.91e+01 dihedral pdb=" O4' A a 560 " pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" C2' A a 560 " ideal model delta sinusoidal sigma weight residual 24.00 -29.69 53.69 1 8.00e+00 1.56e-02 6.12e+01 ... (remaining 7885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 2263 0.202 - 0.405: 12 0.405 - 0.607: 2 0.607 - 0.809: 3 0.809 - 1.012: 1 Chirality restraints: 2281 Sorted by residual: chirality pdb=" P C a 528 " pdb=" OP1 C a 528 " pdb=" OP2 C a 528 " pdb=" O5' C a 528 " both_signs ideal model delta sigma weight residual True 2.41 -3.42 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C3' G a1064 " pdb=" C4' G a1064 " pdb=" O3' G a1064 " pdb=" C2' G a1064 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C3' A a 913 " pdb=" C4' A a 913 " pdb=" O3' A a 913 " pdb=" C2' A a 913 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2278 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 a1519 " 0.123 2.00e-02 2.50e+03 2.01e-01 4.02e+02 pdb=" N6 MA6 a1519 " -0.347 2.00e-02 2.50e+03 pdb=" C10 MA6 a1519 " 0.114 2.00e-02 2.50e+03 pdb=" C9 MA6 a1519 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 a1518 " 0.112 2.00e-02 2.50e+03 1.84e-01 3.40e+02 pdb=" N6 MA6 a1518 " -0.319 2.00e-02 2.50e+03 pdb=" C10 MA6 a1518 " 0.105 2.00e-02 2.50e+03 pdb=" C9 MA6 a1518 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL e 88 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C VAL e 88 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL e 88 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS e 89 " 0.015 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 2 2.42 - 3.04: 4981 3.04 - 3.66: 20335 3.66 - 4.28: 30744 4.28 - 4.90: 42343 Nonbonded interactions: 98405 Sorted by model distance: nonbonded pdb=" N4 C a 528 " pdb=" OD1 ASN l 46 " model vdw 1.797 3.120 nonbonded pdb=" CB LYS l 44 " pdb=" CD PRO l 45 " model vdw 2.219 3.840 nonbonded pdb=" CE LYS w 8 " pdb=" O HIS w 21 " model vdw 2.448 3.440 nonbonded pdb=" O2' U a 921 " pdb=" O THR e 24 " model vdw 2.505 3.040 nonbonded pdb=" O2' A a 560 " pdb=" OP2 U a 561 " model vdw 2.505 3.040 ... (remaining 98400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.008 0.124 12278 Z= 0.497 Angle : 1.064 18.866 18189 Z= 0.687 Chirality : 0.079 1.012 2281 Planarity : 0.009 0.201 1063 Dihedral : 24.006 179.111 6954 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % Rotamer: Outliers : 2.82 % Allowed : 9.65 % Favored : 87.53 % Cbeta Deviations : 0.43 % 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: -2.95 (0.28), residues: 510 helix: -2.54 (0.31), residues: 110 sheet: -0.97 (0.40), residues: 133 loop : -2.22 (0.27), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG v 200 TYR 0.009 0.001 TYR l 95 PHE 0.007 0.001 PHE e 48 TRP 0.007 0.001 TRP v 319 HIS 0.002 0.001 HIS w 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.50 (12278) covalent geometry : angle 1.06420 / 0.69 (18189) hydrogen bonds : bond 0.21675 / 22.74 ( 390) hydrogen bonds : angle 9.99407 / 12.68 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 71 MET cc_start: 0.6939 (ttt) cc_final: 0.6588 (ppp) REVERT: e 95 PHE cc_start: 0.9031 (t80) cc_final: 0.8819 (t80) REVERT: e 122 ASN cc_start: 0.8446 (m-40) cc_final: 0.8067 (m110) REVERT: l 9 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7260 (mtt90) REVERT: l 77 HIS cc_start: 0.7370 (m90) cc_final: 0.7092 (m-70) REVERT: l 112 GLN cc_start: 0.8065 (mt0) cc_final: 0.7738 (mt0) REVERT: w 17 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7620 (tm-30) outliers start: 12 outliers final: 3 residues processed: 133 average time/residue: 0.1417 time to fit residues: 24.5821 Evaluate side-chains 113 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 122 ASN l 5 ASN v 214 HIS w 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.162055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.137326 restraints weight = 15970.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.140910 restraints weight = 5895.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.142955 restraints weight = 3505.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.144162 restraints weight = 2703.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.144706 restraints weight = 2347.674| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12278 Z= 0.164 Angle : 0.666 8.743 18189 Z= 0.380 Chirality : 0.048 0.534 2281 Planarity : 0.005 0.051 1063 Dihedral : 23.950 173.205 5949 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.67 % Rotamer: Outliers : 3.06 % Allowed : 14.59 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.31), residues: 510 helix: 0.28 (0.43), residues: 119 sheet: -0.58 (0.41), residues: 136 loop : -2.26 (0.28), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 20 TYR 0.014 0.002 TYR d 51 PHE 0.013 0.002 PHE w 25 TRP 0.006 0.001 TRP v 319 HIS 0.013 0.002 HIS e 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (12278) covalent geometry : angle 0.66575 / 0.38 (18189) hydrogen bonds : bond 0.07927 / 8.64 ( 390) hydrogen bonds : angle 4.26970 / 5.42 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 122 ASN cc_start: 0.8624 (m110) cc_final: 0.8350 (m110) REVERT: v 147 MET cc_start: 0.7545 (mtm) cc_final: 0.7205 (mtm) REVERT: w 17 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7237 (tm-30) outliers start: 13 outliers final: 5 residues processed: 121 average time/residue: 0.1362 time to fit residues: 21.9797 Evaluate side-chains 119 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [71, 11, 13, 63, 43, 78, 10, 29, 37, 20, 5] chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 36 GLN e 78 ASN l 5 ASN l 6 GLN l 96 HIS w 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.127294 restraints weight = 16481.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.130569 restraints weight = 5854.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132559 restraints weight = 3456.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133631 restraints weight = 2641.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134022 restraints weight = 2311.094| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 12278 Z= 0.525 Angle : 1.207 14.416 18189 Z= 0.585 Chirality : 0.078 0.700 2281 Planarity : 0.010 0.120 1063 Dihedral : 24.141 176.737 5947 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.88 % Favored : 93.92 % Rotamer: Outliers : 7.76 % Allowed : 16.71 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -2.26 (0.33), residues: 510 helix: -0.54 (0.40), residues: 127 sheet: -1.11 (0.43), residues: 129 loop : -2.23 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 45 TYR 0.028 0.003 TYR e 128 PHE 0.023 0.004 PHE w 25 TRP 0.008 0.002 TRP c 167 HIS 0.007 0.003 HIS d 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00880 / 0.53 (12278) covalent geometry : angle 1.20658 / 0.58 (18189) hydrogen bonds : bond 0.12254 / 12.91 ( 390) hydrogen bonds : angle 4.88059 / 6.13 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 122 ASN cc_start: 0.8767 (m110) cc_final: 0.8554 (m110) REVERT: l 6 GLN cc_start: 0.9187 (tt0) cc_final: 0.8923 (tt0) REVERT: l 31 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6030 (ptp90) REVERT: l 67 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8603 (mp) REVERT: l 98 VAL cc_start: 0.9561 (t) cc_final: 0.9117 (p) REVERT: l 116 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8556 (ttmm) REVERT: l 119 VAL cc_start: 0.9083 (t) cc_final: 0.8728 (m) REVERT: v 147 MET cc_start: 0.7807 (mtm) cc_final: 0.7409 (mtm) REVERT: v 323 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7336 (tt) REVERT: w 17 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: w 21 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8031 (t-90) REVERT: w 45 HIS cc_start: 0.8165 (m-70) cc_final: 0.7742 (m170) outliers start: 33 outliers final: 19 residues processed: 157 average time/residue: 0.1350 time to fit residues: 27.8272 Evaluate side-chains 158 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 85 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 105 SER Chi-restraints excluded: chain v residue 139 THR Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain v residue 325 SER Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [47, 43, 31, 10, 51, 22, 79, 28, 58, 26, 80] chunk 47 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.159340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.135919 restraints weight = 16211.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139371 restraints weight = 5954.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.141418 restraints weight = 3508.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.142404 restraints weight = 2677.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.143101 restraints weight = 2354.009| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12278 Z= 0.141 Angle : 0.628 8.613 18189 Z= 0.354 Chirality : 0.044 0.556 2281 Planarity : 0.005 0.071 1063 Dihedral : 24.132 171.671 5947 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.92 % Favored : 95.88 % Rotamer: Outliers : 5.88 % Allowed : 22.12 % Favored : 72.00 % 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: -1.77 (0.34), residues: 510 helix: 0.40 (0.44), residues: 129 sheet: -1.00 (0.43), residues: 134 loop : -2.17 (0.33), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG l 54 TYR 0.016 0.002 TYR l 66 PHE 0.016 0.002 PHE e 48 TRP 0.008 0.001 TRP v 155 HIS 0.003 0.001 HIS d 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (12278) covalent geometry : angle 0.62849 / 0.35 (18189) hydrogen bonds : bond 0.07673 / 8.50 ( 390) hydrogen bonds : angle 4.01376 / 4.94 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 169 ARG cc_start: 0.4697 (OUTLIER) cc_final: 0.4496 (ttt-90) REVERT: e 64 MET cc_start: 0.7279 (tmm) cc_final: 0.6911 (tmm) REVERT: e 122 ASN cc_start: 0.8652 (m110) cc_final: 0.8414 (m110) REVERT: l 15 LYS cc_start: 0.7613 (mtmt) cc_final: 0.6804 (mttt) REVERT: l 36 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7547 (ttm110) REVERT: l 98 VAL cc_start: 0.9408 (t) cc_final: 0.8859 (p) REVERT: l 119 VAL cc_start: 0.8859 (t) cc_final: 0.8501 (m) REVERT: v 147 MET cc_start: 0.7605 (mtm) cc_final: 0.7158 (mtm) REVERT: v 323 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7237 (tt) REVERT: w 4 TYR cc_start: 0.8641 (t80) cc_final: 0.8439 (t80) REVERT: w 17 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7266 (tm-30) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 0.1537 time to fit residues: 28.9729 Evaluate side-chains 143 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 205 SER Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [40, 37, 27, 53, 43, 32, 50, 45, 66, 51, 56] chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... v 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.159302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135821 restraints weight = 16147.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.139341 restraints weight = 5667.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.141458 restraints weight = 3295.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.142446 restraints weight = 2472.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.143239 restraints weight = 2168.794| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12278 Z= 0.156 Angle : 0.621 9.518 18189 Z= 0.342 Chirality : 0.044 0.545 2281 Planarity : 0.006 0.074 1063 Dihedral : 23.765 172.877 5947 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.73 % Favored : 96.08 % Rotamer: Outliers : 5.88 % Allowed : 24.24 % Favored : 69.88 % 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: -1.61 (0.34), residues: 510 helix: 0.56 (0.43), residues: 131 sheet: -1.00 (0.43), residues: 130 loop : -2.03 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 9 TYR 0.012 0.001 TYR l 66 PHE 0.010 0.002 PHE w 25 TRP 0.008 0.001 TRP v 155 HIS 0.003 0.001 HIS e 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (12278) covalent geometry : angle 0.62092 / 0.34 (18189) hydrogen bonds : bond 0.06844 / 7.34 ( 390) hydrogen bonds : angle 3.83059 / 4.70 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 169 ARG cc_start: 0.4716 (OUTLIER) cc_final: 0.4489 (ttt-90) REVERT: e 64 MET cc_start: 0.7246 (tmm) cc_final: 0.7015 (tmm) REVERT: e 122 ASN cc_start: 0.8705 (m110) cc_final: 0.8470 (m110) REVERT: l 15 LYS cc_start: 0.7565 (mtmt) cc_final: 0.6856 (mttt) REVERT: v 147 MET cc_start: 0.7601 (mtm) cc_final: 0.7180 (mtm) REVERT: v 164 GLU cc_start: 0.7652 (mp0) cc_final: 0.6960 (pm20) REVERT: v 323 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7241 (tt) REVERT: w 21 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8404 (t-90) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.1344 time to fit residues: 24.4377 Evaluate side-chains 140 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 85 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 205 SER Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [67, 60, 62, 65, 7, 0, 30, 36, 23, 40, 4] chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.128268 restraints weight = 16507.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.131593 restraints weight = 5815.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.133631 restraints weight = 3435.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.134657 restraints weight = 2630.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135132 restraints weight = 2306.444| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12278 Z= 0.444 Angle : 1.039 12.177 18189 Z= 0.505 Chirality : 0.070 0.686 2281 Planarity : 0.008 0.106 1063 Dihedral : 23.767 174.382 5944 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.49 % Favored : 94.31 % Rotamer: Outliers : 8.00 % Allowed : 24.24 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.33), residues: 510 helix: -0.35 (0.41), residues: 129 sheet: -1.49 (0.43), residues: 123 loop : -2.23 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG v 212 TYR 0.022 0.003 TYR e 128 PHE 0.021 0.004 PHE w 25 TRP 0.008 0.002 TRP v 155 HIS 0.008 0.003 HIS l 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.44 (12278) covalent geometry : angle 1.03938 / 0.51 (18189) hydrogen bonds : bond 0.10417 / 10.98 ( 390) hydrogen bonds : angle 4.48930 / 5.57 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 64 MET cc_start: 0.7491 (tmm) cc_final: 0.7207 (tmm) REVERT: e 92 SER cc_start: 0.9429 (m) cc_final: 0.9203 (m) REVERT: e 112 ARG cc_start: 0.8933 (ptm160) cc_final: 0.8577 (ptm160) REVERT: e 122 ASN cc_start: 0.8820 (m110) cc_final: 0.8593 (m110) REVERT: l 15 LYS cc_start: 0.7514 (mtmt) cc_final: 0.6986 (mttt) REVERT: l 31 ARG cc_start: 0.7194 (ttp80) cc_final: 0.5997 (ptp90) REVERT: l 114 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5421 (ptt90) REVERT: l 119 VAL cc_start: 0.9084 (t) cc_final: 0.8721 (m) REVERT: v 147 MET cc_start: 0.7782 (mtm) cc_final: 0.7330 (mtm) REVERT: v 323 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7362 (tt) REVERT: w 21 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8217 (t-90) REVERT: w 45 HIS cc_start: 0.7932 (m-70) cc_final: 0.7554 (m170) outliers start: 34 outliers final: 24 residues processed: 141 average time/residue: 0.1415 time to fit residues: 25.9291 Evaluate side-chains 147 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 85 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain v residue 176 ILE Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 205 SER Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 319 TRP Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain v residue 327 VAL Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [55, 51, 56, 81, 44, 40, 75, 14, 30, 45, 64] chunk 55 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 135 ASN w 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.160036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.136500 restraints weight = 16215.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.140083 restraints weight = 5725.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.142158 restraints weight = 3312.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.143288 restraints weight = 2511.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.143735 restraints weight = 2173.371| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12278 Z= 0.136 Angle : 0.620 9.994 18189 Z= 0.346 Chirality : 0.043 0.560 2281 Planarity : 0.006 0.072 1063 Dihedral : 23.827 171.547 5944 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.31 % Favored : 95.49 % Rotamer: Outliers : 4.94 % Allowed : 26.12 % Favored : 68.94 % 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: -2.02 (0.34), residues: 510 helix: 0.10 (0.42), residues: 130 sheet: -1.46 (0.41), residues: 131 loop : -2.06 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG v 200 TYR 0.018 0.002 TYR l 66 PHE 0.007 0.002 PHE l 61 TRP 0.009 0.001 TRP v 155 HIS 0.003 0.001 HIS d 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (12278) covalent geometry : angle 0.62009 / 0.35 (18189) hydrogen bonds : bond 0.07270 / 7.99 ( 390) hydrogen bonds : angle 3.92000 / 4.84 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 50 TYR cc_start: 0.8220 (t80) cc_final: 0.7997 (t80) REVERT: e 52 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7390 (mtmm) REVERT: e 64 MET cc_start: 0.7246 (tmm) cc_final: 0.7012 (tmm) REVERT: e 122 ASN cc_start: 0.8613 (m110) cc_final: 0.8406 (m110) REVERT: l 15 LYS cc_start: 0.7396 (mtmt) cc_final: 0.6884 (mttt) REVERT: l 119 VAL cc_start: 0.8917 (t) cc_final: 0.8609 (m) REVERT: v 147 MET cc_start: 0.7469 (mtm) cc_final: 0.7052 (mtm) REVERT: v 164 GLU cc_start: 0.7855 (mp0) cc_final: 0.7163 (pm20) REVERT: v 182 LYS cc_start: 0.8495 (tptp) cc_final: 0.8219 (tptp) REVERT: v 323 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7248 (tt) REVERT: w 21 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8318 (t-90) outliers start: 21 outliers final: 16 residues processed: 139 average time/residue: 0.1280 time to fit residues: 23.7090 Evaluate side-chains 139 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 205 SER Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [52, 15, 48, 57, 64, 6, 70, 4, 7, 38, 3] chunk 52 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.129850 restraints weight = 16357.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.133233 restraints weight = 5707.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.135238 restraints weight = 3327.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136198 restraints weight = 2532.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.136347 restraints weight = 2237.368| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12278 Z= 0.390 Angle : 0.948 9.483 18189 Z= 0.469 Chirality : 0.065 0.648 2281 Planarity : 0.008 0.100 1063 Dihedral : 23.739 173.801 5944 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.67 % Favored : 93.14 % Rotamer: Outliers : 6.35 % Allowed : 26.59 % Favored : 67.06 % 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: -2.48 (0.33), residues: 510 helix: -0.40 (0.41), residues: 130 sheet: -1.77 (0.41), residues: 127 loop : -2.25 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG w 41 TYR 0.020 0.003 TYR e 128 PHE 0.016 0.003 PHE w 25 TRP 0.009 0.002 TRP v 155 HIS 0.007 0.002 HIS v 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.39 (12278) covalent geometry : angle 0.94817 / 0.47 (18189) hydrogen bonds : bond 0.09687 / 10.25 ( 390) hydrogen bonds : angle 4.29236 / 5.38 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 9 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6635 (mt) REVERT: e 13 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7846 (tm-30) REVERT: e 50 TYR cc_start: 0.8360 (t80) cc_final: 0.8087 (t80) REVERT: e 52 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7548 (mtmm) REVERT: e 64 MET cc_start: 0.7426 (tmm) cc_final: 0.7007 (tmm) REVERT: e 112 ARG cc_start: 0.8957 (ptm160) cc_final: 0.8594 (ptm160) REVERT: l 15 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7137 (mttt) REVERT: l 31 ARG cc_start: 0.7196 (ttp80) cc_final: 0.5918 (ptp90) REVERT: l 119 VAL cc_start: 0.9099 (t) cc_final: 0.8763 (m) REVERT: v 147 MET cc_start: 0.7731 (mtm) cc_final: 0.7237 (mtm) REVERT: v 323 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7367 (tt) REVERT: w 21 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8457 (t-90) REVERT: w 45 HIS cc_start: 0.7904 (m-70) cc_final: 0.7540 (m170) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.1464 time to fit residues: 25.3457 Evaluate side-chains 140 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 70 GLU Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 205 SER Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 319 TRP Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [37, 1, 79, 8, 39, 61, 72, 7, 35, 65, 10] chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.157855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134686 restraints weight = 16097.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.138001 restraints weight = 5828.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.140062 restraints weight = 3464.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.141009 restraints weight = 2622.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.141652 restraints weight = 2307.568| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12278 Z= 0.213 Angle : 0.696 11.503 18189 Z= 0.375 Chirality : 0.048 0.604 2281 Planarity : 0.006 0.072 1063 Dihedral : 23.797 172.352 5944 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.88 % Favored : 93.92 % Rotamer: Outliers : 4.47 % Allowed : 28.47 % Favored : 67.06 % 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: -2.45 (0.33), residues: 510 helix: -0.32 (0.42), residues: 130 sheet: -1.84 (0.40), residues: 126 loop : -2.21 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG l 9 TYR 0.016 0.002 TYR l 66 PHE 0.010 0.002 PHE w 25 TRP 0.009 0.001 TRP v 155 HIS 0.006 0.001 HIS d 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.21 (12278) covalent geometry : angle 0.69641 / 0.37 (18189) hydrogen bonds : bond 0.08006 / 8.65 ( 390) hydrogen bonds : angle 4.03473 / 5.08 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 156 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7721 (mtt-85) REVERT: d 9 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6589 (mt) REVERT: e 13 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7781 (tm-30) REVERT: e 50 TYR cc_start: 0.8312 (t80) cc_final: 0.7918 (t80) REVERT: e 64 MET cc_start: 0.7308 (tmm) cc_final: 0.6905 (tmm) REVERT: e 112 ARG cc_start: 0.8804 (ptm160) cc_final: 0.8416 (ptm160) REVERT: l 15 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7063 (mttt) REVERT: l 31 ARG cc_start: 0.7104 (ttp80) cc_final: 0.5826 (ptp90) REVERT: l 119 VAL cc_start: 0.9029 (t) cc_final: 0.8714 (m) REVERT: v 147 MET cc_start: 0.7657 (mtm) cc_final: 0.7184 (mtm) REVERT: v 323 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7470 (tt) REVERT: w 21 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.8462 (t-90) REVERT: w 26 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8316 (ttm170) REVERT: w 45 HIS cc_start: 0.7734 (m-70) cc_final: 0.7435 (m170) outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 0.1430 time to fit residues: 24.9755 Evaluate side-chains 134 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 205 SER Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [24, 31, 46, 21, 49, 42, 23, 61, 1, 40, 33] chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 61 optimal weight: 0.0670 chunk 1 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 overall best weight: 1.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 41 HIS ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.160142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136964 restraints weight = 16191.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140383 restraints weight = 5846.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142461 restraints weight = 3426.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.143549 restraints weight = 2586.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.143819 restraints weight = 2246.991| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12278 Z= 0.168 Angle : 0.630 9.118 18189 Z= 0.344 Chirality : 0.044 0.533 2281 Planarity : 0.006 0.070 1063 Dihedral : 23.673 171.940 5944 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.29 % Favored : 94.51 % Rotamer: Outliers : 3.53 % Allowed : 29.41 % Favored : 67.06 % 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: -2.24 (0.33), residues: 510 helix: -0.11 (0.44), residues: 130 sheet: -1.76 (0.41), residues: 123 loop : -2.07 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG l 9 TYR 0.016 0.002 TYR l 66 PHE 0.018 0.002 PHE e 95 TRP 0.009 0.001 TRP v 155 HIS 0.004 0.001 HIS d 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (12278) covalent geometry : angle 0.62986 / 0.34 (18189) hydrogen bonds : bond 0.06942 / 7.55 ( 390) hydrogen bonds : angle 3.80809 / 4.80 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 156 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7873 (mtt-85) REVERT: e 13 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7695 (tm-30) REVERT: e 50 TYR cc_start: 0.8241 (t80) cc_final: 0.7734 (t80) REVERT: e 64 MET cc_start: 0.7240 (tmm) cc_final: 0.6901 (tmm) REVERT: l 15 LYS cc_start: 0.7610 (mtmt) cc_final: 0.7090 (mttt) REVERT: l 31 ARG cc_start: 0.6939 (ttp80) cc_final: 0.5821 (ptp90) REVERT: l 119 VAL cc_start: 0.8973 (t) cc_final: 0.8684 (m) REVERT: v 147 MET cc_start: 0.7512 (mtm) cc_final: 0.7149 (mtm) REVERT: v 323 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7215 (tt) REVERT: w 21 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8500 (t-90) REVERT: w 26 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8381 (ttm170) REVERT: w 45 HIS cc_start: 0.7666 (m-70) cc_final: 0.7407 (m170) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.1439 time to fit residues: 23.6130 Evaluate side-chains 131 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain v residue 179 VAL Chi-restraints excluded: chain v residue 313 ASN Chi-restraints excluded: chain v residue 323 ILE Chi-restraints excluded: chain w residue 20 LEU Chi-restraints excluded: chain w residue 21 HIS Chi-restraints excluded: chain w residue 22 ASP Chi-restraints excluded: chain w residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [8, 57, 20, 23, 7, 30, 3, 13, 76, 61, 12] chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.153247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.129644 restraints weight = 16354.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.132953 restraints weight = 5744.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.134946 restraints weight = 3386.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.135862 restraints weight = 2579.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.136592 restraints weight = 2276.644| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 12278 Z= 0.436 Angle : 1.026 11.051 18189 Z= 0.497 Chirality : 0.067 0.645 2281 Planarity : 0.008 0.094 1063 Dihedral : 23.716 173.528 5944 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.65 % Favored : 92.16 % Rotamer: Outliers : 4.71 % Allowed : 28.24 % Favored : 67.06 % 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: -2.81 (0.32), residues: 510 helix: -0.91 (0.41), residues: 136 sheet: -2.07 (0.40), residues: 122 loop : -2.27 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG v 212 TYR 0.024 0.003 TYR e 128 PHE 0.018 0.003 PHE w 25 TRP 0.009 0.002 TRP v 155 HIS 0.008 0.003 HIS d 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.44 (12278) covalent geometry : angle 1.02604 / 0.50 (18189) hydrogen bonds : bond 0.10053 / 10.64 ( 390) hydrogen bonds : angle 4.36837 / 5.54 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.64 seconds wall clock time: 29 minutes 31.00 seconds (1771.00 seconds total)