Starting phenix.real_space_refine on Thu Mar 6 08:02:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xla_22237/03_2025/6xla_22237.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xla_22237/03_2025/6xla_22237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xla_22237/03_2025/6xla_22237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xla_22237/03_2025/6xla_22237.map" model { file = "/net/cci-nas-00/data/ceres_data/6xla_22237/03_2025/6xla_22237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xla_22237/03_2025/6xla_22237.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 6 Type Number sf(0) Gaussians Sb 2 10.97 5 P 44 5.49 5 S 26 5.16 5 C 3339 2.51 5 N 912 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5403 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "N" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.88 Number of scatterers: 5403 At special positions: 0 Unit cell: (116.35, 104.715, 71.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sb 2 50.95 S 26 16.00 P 44 15.00 O 1080 8.00 N 912 7.00 C 3339 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: 1.33 Conformation dependent library (CDL) restraints added in 688.3 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 46.3% alpha, 27.6% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.607A pdb=" N LYS G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.523A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.675A pdb=" N LEU G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 75 through 110 removed outlier: 3.707A pdb=" N GLU G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 80 " --> pdb=" O HIS G 76 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 81 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 153 Proline residue: G 144 - end of helix removed outlier: 3.594A pdb=" N VAL G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 removed outlier: 3.930A pdb=" N SER G 218 " --> pdb=" O PRO G 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 215 through 218' Processing helix chain 'G' and resid 219 through 233 removed outlier: 3.633A pdb=" N TYR G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU G 231 " --> pdb=" O MET G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 Processing helix chain 'H' and resid 3 through 12 removed outlier: 3.646A pdb=" N LYS H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.835A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.919A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 removed outlier: 4.039A pdb=" N GLN H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 109 removed outlier: 4.107A pdb=" N GLU H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU H 109 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 removed outlier: 3.865A pdb=" N TYR H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 154 removed outlier: 3.830A pdb=" N GLY H 147 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 233 removed outlier: 4.256A pdb=" N ALA H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET H 227 " --> pdb=" O TYR H 223 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU H 231 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 257 Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.555A pdb=" N TYR G 31 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.472A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.472A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.457A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.457A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2328 1.40 - 1.58: 3160 1.58 - 1.77: 88 1.77 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5626 Sorted by residual: bond pdb="SB 118 G 301 " pdb=" C1C 118 G 301 " ideal model delta sigma weight residual 2.092 2.134 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb="SB 118 G 301 " pdb=" C1D 118 G 301 " ideal model delta sigma weight residual 2.092 2.131 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb="SB 118 H 301 " pdb=" C1C 118 H 301 " ideal model delta sigma weight residual 2.092 2.130 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb="SB 118 H 301 " pdb=" C1D 118 H 301 " ideal model delta sigma weight residual 2.092 2.129 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb="SB 118 G 301 " pdb=" C1A 118 G 301 " ideal model delta sigma weight residual 2.093 2.129 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 5621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 7558 1.63 - 3.26: 227 3.26 - 4.89: 22 4.89 - 6.52: 5 6.52 - 8.16: 1 Bond angle restraints: 7813 Sorted by residual: angle pdb=" N ILE G 143 " pdb=" CA ILE G 143 " pdb=" C ILE G 143 " ideal model delta sigma weight residual 108.88 117.04 -8.16 2.16e+00 2.14e-01 1.43e+01 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 115.28 -4.58 1.22e+00 6.72e-01 1.41e+01 angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.33 -4.13 1.50e+00 4.44e-01 7.60e+00 angle pdb=" CA ILE G 143 " pdb=" C ILE G 143 " pdb=" N PRO G 144 " ideal model delta sigma weight residual 118.88 122.79 -3.91 1.54e+00 4.22e-01 6.44e+00 angle pdb=" N ILE H 143 " pdb=" CA ILE H 143 " pdb=" C ILE H 143 " ideal model delta sigma weight residual 108.88 114.23 -5.35 2.16e+00 2.14e-01 6.14e+00 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 2958 31.48 - 62.95: 253 62.95 - 94.43: 14 94.43 - 125.91: 0 125.91 - 157.38: 1 Dihedral angle restraints: 3226 sinusoidal: 1630 harmonic: 1596 Sorted by residual: dihedral pdb=" CA VAL H 126 " pdb=" C VAL H 126 " pdb=" N TYR H 127 " pdb=" CA TYR H 127 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ILE H 143 " pdb=" C ILE H 143 " pdb=" N PRO H 144 " pdb=" CA PRO H 144 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sinusoidal sigma weight residual 220.00 62.62 157.38 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 3223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 493 0.031 - 0.063: 250 0.063 - 0.094: 75 0.094 - 0.125: 24 0.125 - 0.156: 12 Chirality restraints: 854 Sorted by residual: chirality pdb=" CA ILE H 132 " pdb=" N ILE H 132 " pdb=" C ILE H 132 " pdb=" CB ILE H 132 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL H 210 " pdb=" N VAL H 210 " pdb=" C VAL H 210 " pdb=" CB VAL H 210 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CB ILE G 143 " pdb=" CA ILE G 143 " pdb=" CG1 ILE G 143 " pdb=" CG2 ILE G 143 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 851 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 144 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO H 145 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 145 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 145 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 51 " -0.024 2.00e-02 2.50e+03 1.01e-02 2.82e+00 pdb=" N9 DA N 51 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA N 51 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA N 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N 51 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA N 51 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA N 51 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA N 51 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA N 51 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA N 51 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO G 145 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " 0.023 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1288 2.80 - 3.33: 4457 3.33 - 3.85: 8610 3.85 - 4.38: 10617 4.38 - 4.90: 16575 Nonbonded interactions: 41547 Sorted by model distance: nonbonded pdb=" OH TYR G 127 " pdb=" OE1 GLU G 185 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR H 61 " pdb=" OE1 GLU H 64 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR G 61 " pdb=" OE2 GLU G 64 " model vdw 2.305 3.040 nonbonded pdb=" N6 DA N 51 " pdb=" O4 DT T 38 " model vdw 2.332 3.120 nonbonded pdb=" NZ LYS H 108 " pdb=" OE2 GLU H 109 " model vdw 2.358 3.120 ... (remaining 41542 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 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'N' and (resid 41 through 50 or resid 52 through 61)) selection = (chain 'T' and (resid 28 through 37 or resid 39 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.180 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5626 Z= 0.298 Angle : 0.651 8.156 7813 Z= 0.387 Chirality : 0.043 0.156 854 Planarity : 0.005 0.062 832 Dihedral : 19.958 157.382 2198 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.32), residues: 532 helix: -1.71 (0.29), residues: 216 sheet: -0.87 (0.48), residues: 104 loop : -1.99 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 229 HIS 0.004 0.001 HIS G 101 PHE 0.017 0.002 PHE G 131 TYR 0.019 0.001 TYR G 127 ARG 0.002 0.000 ARG G 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: G 192 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6500 (mtmt) REVERT: H 105 HIS cc_start: 0.7643 (t70) cc_final: 0.7331 (t-90) REVERT: H 232 ASP cc_start: 0.7786 (t0) cc_final: 0.7506 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2738 time to fit residues: 21.7890 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 105 HIS G 178 ASN G 233 ASN H 3 GLN H 33 ASN H 101 HIS H 105 HIS H 233 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106458 restraints weight = 5429.375| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.39 r_work: 0.3316 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5626 Z= 0.221 Angle : 0.562 6.879 7813 Z= 0.325 Chirality : 0.041 0.145 854 Planarity : 0.004 0.056 832 Dihedral : 21.776 157.029 1084 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.02 % Allowed : 9.59 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.35), residues: 532 helix: 0.36 (0.34), residues: 218 sheet: -0.92 (0.47), residues: 112 loop : -1.67 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 229 HIS 0.008 0.001 HIS G 105 PHE 0.013 0.001 PHE G 131 TYR 0.014 0.001 TYR G 127 ARG 0.003 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.514 Fit side-chains REVERT: G 192 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6429 (mtmt) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.1744 time to fit residues: 12.6846 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN G 105 HIS H 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109300 restraints weight = 5525.804| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.41 r_work: 0.3358 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.165 Angle : 0.519 6.331 7813 Z= 0.300 Chirality : 0.039 0.143 854 Planarity : 0.004 0.051 832 Dihedral : 21.559 156.725 1084 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.61 % Allowed : 11.22 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.36), residues: 532 helix: 1.24 (0.35), residues: 224 sheet: -0.26 (0.53), residues: 98 loop : -1.43 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 229 HIS 0.010 0.001 HIS G 105 PHE 0.011 0.001 PHE G 131 TYR 0.010 0.001 TYR G 127 ARG 0.002 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.542 Fit side-chains REVERT: G 192 LYS cc_start: 0.7052 (mmtt) cc_final: 0.6338 (mtmt) REVERT: G 227 MET cc_start: 0.8487 (mmm) cc_final: 0.8233 (mmt) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.1891 time to fit residues: 13.8751 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.0030 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.129993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109433 restraints weight = 5565.294| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.42 r_work: 0.3361 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.165 Angle : 0.511 6.088 7813 Z= 0.294 Chirality : 0.038 0.145 854 Planarity : 0.004 0.046 832 Dihedral : 21.480 156.477 1084 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.43 % Allowed : 12.65 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.37), residues: 532 helix: 1.66 (0.35), residues: 224 sheet: -0.15 (0.54), residues: 98 loop : -1.41 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 229 HIS 0.003 0.001 HIS H 105 PHE 0.011 0.001 PHE G 131 TYR 0.011 0.001 TYR G 127 ARG 0.003 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.506 Fit side-chains REVERT: G 192 LYS cc_start: 0.7032 (mmtt) cc_final: 0.6320 (mtmt) REVERT: G 227 MET cc_start: 0.8463 (mmm) cc_final: 0.8218 (mmt) outliers start: 7 outliers final: 3 residues processed: 61 average time/residue: 0.1797 time to fit residues: 14.4108 Evaluate side-chains 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 ASN H 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106660 restraints weight = 5432.442| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.44 r_work: 0.3316 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.228 Angle : 0.562 8.074 7813 Z= 0.317 Chirality : 0.040 0.148 854 Planarity : 0.004 0.044 832 Dihedral : 21.657 157.260 1084 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.43 % Allowed : 14.08 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.36), residues: 532 helix: 1.60 (0.35), residues: 226 sheet: -0.34 (0.53), residues: 100 loop : -1.61 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 229 HIS 0.004 0.001 HIS H 105 PHE 0.011 0.002 PHE H 49 TYR 0.014 0.001 TYR H 127 ARG 0.002 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.559 Fit side-chains REVERT: G 192 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6321 (mtmt) REVERT: G 227 MET cc_start: 0.8494 (mmm) cc_final: 0.8231 (mmt) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 0.1798 time to fit residues: 13.0861 Evaluate side-chains 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107354 restraints weight = 5472.766| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.45 r_work: 0.3324 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.200 Angle : 0.539 7.606 7813 Z= 0.306 Chirality : 0.039 0.146 854 Planarity : 0.003 0.043 832 Dihedral : 21.565 156.861 1084 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.63 % Allowed : 14.90 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.37), residues: 532 helix: 1.87 (0.35), residues: 224 sheet: -0.17 (0.54), residues: 96 loop : -1.47 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 229 HIS 0.004 0.001 HIS H 105 PHE 0.012 0.001 PHE H 136 TYR 0.013 0.001 TYR G 127 ARG 0.002 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.554 Fit side-chains REVERT: G 192 LYS cc_start: 0.6977 (mmtt) cc_final: 0.6276 (mtmt) REVERT: G 227 MET cc_start: 0.8484 (mmm) cc_final: 0.8225 (mmt) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.1858 time to fit residues: 12.9688 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 GLN Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110446 restraints weight = 5642.905| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.40 r_work: 0.3398 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.225 Angle : 0.561 11.664 7813 Z= 0.314 Chirality : 0.040 0.148 854 Planarity : 0.004 0.043 832 Dihedral : 21.644 157.400 1084 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.63 % Allowed : 15.71 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.37), residues: 532 helix: 1.90 (0.35), residues: 224 sheet: -0.31 (0.53), residues: 100 loop : -1.52 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 PHE 0.011 0.001 PHE H 49 TYR 0.014 0.001 TYR G 127 ARG 0.003 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.498 Fit side-chains REVERT: G 192 LYS cc_start: 0.7033 (mmtt) cc_final: 0.6388 (mtmt) REVERT: G 227 MET cc_start: 0.8426 (mmm) cc_final: 0.8200 (mmt) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.1844 time to fit residues: 13.0673 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110858 restraints weight = 5639.973| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.39 r_work: 0.3405 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.211 Angle : 0.556 10.432 7813 Z= 0.312 Chirality : 0.040 0.147 854 Planarity : 0.004 0.044 832 Dihedral : 21.596 157.299 1084 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.43 % Allowed : 15.71 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.37), residues: 532 helix: 1.95 (0.35), residues: 224 sheet: -0.12 (0.48), residues: 126 loop : -1.74 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS H 105 PHE 0.010 0.001 PHE G 131 TYR 0.013 0.001 TYR G 127 ARG 0.003 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.507 Fit side-chains REVERT: G 192 LYS cc_start: 0.6987 (mmtt) cc_final: 0.6346 (mtmt) REVERT: G 227 MET cc_start: 0.8414 (mmm) cc_final: 0.8191 (mmt) outliers start: 7 outliers final: 7 residues processed: 52 average time/residue: 0.1801 time to fit residues: 12.4103 Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 GLN Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111317 restraints weight = 5622.994| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.40 r_work: 0.3415 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5626 Z= 0.191 Angle : 0.546 8.791 7813 Z= 0.307 Chirality : 0.039 0.151 854 Planarity : 0.004 0.044 832 Dihedral : 21.546 157.239 1084 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.22 % Allowed : 16.12 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.37), residues: 532 helix: 2.04 (0.35), residues: 224 sheet: -0.17 (0.48), residues: 128 loop : -1.69 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 PHE 0.009 0.001 PHE G 131 TYR 0.013 0.001 TYR H 139 ARG 0.003 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.585 Fit side-chains REVERT: G 192 LYS cc_start: 0.7006 (mmtt) cc_final: 0.6359 (mtmt) REVERT: G 227 MET cc_start: 0.8400 (mmm) cc_final: 0.8178 (mmt) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.1903 time to fit residues: 13.2498 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111166 restraints weight = 5634.208| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.41 r_work: 0.3412 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5626 Z= 0.202 Angle : 0.559 11.694 7813 Z= 0.311 Chirality : 0.040 0.154 854 Planarity : 0.004 0.044 832 Dihedral : 21.573 157.250 1084 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.22 % Allowed : 16.33 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.37), residues: 532 helix: 2.02 (0.35), residues: 224 sheet: -0.15 (0.48), residues: 128 loop : -1.71 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 PHE 0.010 0.001 PHE G 136 TYR 0.013 0.001 TYR G 127 ARG 0.003 0.000 ARG H 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.526 Fit side-chains REVERT: G 192 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6366 (mtmt) REVERT: G 227 MET cc_start: 0.8386 (mmm) cc_final: 0.8164 (mmt) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.1941 time to fit residues: 13.1305 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 GLN Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110579 restraints weight = 5629.379| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.41 r_work: 0.3403 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5626 Z= 0.218 Angle : 0.561 10.418 7813 Z= 0.314 Chirality : 0.040 0.149 854 Planarity : 0.004 0.043 832 Dihedral : 21.631 157.479 1084 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.63 % Allowed : 16.12 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.37), residues: 532 helix: 1.96 (0.35), residues: 224 sheet: -0.07 (0.48), residues: 126 loop : -1.71 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 229 HIS 0.003 0.001 HIS H 105 PHE 0.010 0.001 PHE H 49 TYR 0.013 0.001 TYR G 127 ARG 0.003 0.000 ARG H 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.40 seconds wall clock time: 56 minutes 31.42 seconds (3391.42 seconds total)