Starting phenix.real_space_refine on Thu Sep 10 23:59:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlk_22246/09_2026/6xlk_22246.cif" } resolution = 3.3 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= 0.004 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 3386 2.51 5 N 912 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5456 Number of models: 1 Model: "" Number of chains: 6 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: 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: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.40, per 1000 atoms: 0.26 Number of scatterers: 5456 At special positions: 0 Unit cell: (86.645, 115.971, 87.978, 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 1086 8.00 N 912 7.00 C 3386 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: 0.45 Conformation dependent library (CDL) restraints added in 169.8 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, 28.2% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.688A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.941A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.655A 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 74 through 109 removed outlier: 3.868A pdb=" N ILE G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 removed outlier: 3.952A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 154 removed outlier: 3.977A pdb=" N ILE G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 218 through 233 removed outlier: 4.274A pdb=" N ALA G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 14 through 25 Processing helix chain 'H' and resid 42 through 57 removed outlier: 3.540A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 75 through 109 removed outlier: 3.522A pdb=" N GLU H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 154 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 218 through 233 removed outlier: 4.477A pdb=" N ALA H 222 " --> pdb=" O SER H 218 " (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 Processing sheet with id=AA2, first strand: chain 'G' and resid 117 through 121 removed outlier: 4.989A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET G 259 " --> pdb=" O ILE G 246 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 117 through 121 removed outlier: 4.989A 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: 4.518A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 4.856A 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: 4.518A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 2323 1.39 - 1.58: 3224 1.58 - 1.76: 88 1.76 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5685 Sorted by residual: bond pdb=" C3' DC T 29 " pdb=" O3' DC T 29 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.60e+01 bond pdb=" N1 DC N 44 " pdb=" C6 DC N 44 " ideal model delta sigma weight residual 1.367 1.344 0.023 6.00e-03 2.78e+04 1.42e+01 bond pdb=" N1 DC T 31 " pdb=" C6 DC T 31 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.14e+01 bond pdb=" O4' DG T 40 " pdb=" C1' DG T 40 " ideal model delta sigma weight residual 1.420 1.383 0.037 1.10e-02 8.26e+03 1.11e+01 bond pdb=" N1 DC T 30 " pdb=" C6 DC T 30 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 1.05e+01 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 7416 1.54 - 3.07: 435 3.07 - 4.61: 45 4.61 - 6.15: 7 6.15 - 7.68: 5 Bond angle restraints: 7908 Sorted by residual: angle pdb=" O4' DT T 38 " pdb=" C4' DT T 38 " pdb=" C3' DT T 38 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" N3 DT N 45 " pdb=" C4 DT N 45 " pdb=" O4 DT N 45 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT N 62 " pdb=" C4 DT N 62 " pdb=" O4 DT N 62 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" O4' DT N 61 " pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " ideal model delta sigma weight residual 106.00 103.44 2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.85: 2951 31.85 - 63.70: 266 63.70 - 95.54: 13 95.54 - 127.39: 0 127.39 - 159.24: 1 Dihedral angle restraints: 3231 sinusoidal: 1635 harmonic: 1596 Sorted by residual: 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 60.76 159.24 1 3.50e+01 8.16e-04 1.52e+01 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 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR G 114 " pdb=" C TYR G 114 " pdb=" N GLN G 115 " pdb=" CA GLN G 115 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 609 0.050 - 0.100: 201 0.100 - 0.150: 53 0.150 - 0.199: 8 0.199 - 0.249: 5 Chirality restraints: 876 Sorted by residual: chirality pdb=" CB ILE H 125 " pdb=" CA ILE H 125 " pdb=" CG1 ILE H 125 " pdb=" CG2 ILE H 125 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' DC T 29 " pdb=" C4' DC T 29 " pdb=" O3' DC T 29 " pdb=" C2' DC T 29 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C6 1N7 H 301 " pdb=" C18 1N7 H 301 " pdb=" C5 1N7 H 301 " pdb=" C7 1N7 H 301 " both_signs ideal model delta sigma weight residual False -2.43 -2.63 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 873 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO G 145 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 224 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ILE G 224 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE G 224 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR G 225 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 206 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C THR G 206 " 0.026 2.00e-02 2.50e+03 pdb=" O THR G 206 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA G 207 " -0.009 2.00e-02 2.50e+03 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 829 2.75 - 3.29: 5109 3.29 - 3.83: 9692 3.83 - 4.36: 11419 4.36 - 4.90: 18291 Nonbonded interactions: 45340 Sorted by model distance: nonbonded pdb=" NE2 HIS G 170 " pdb=" OE1 GLU G 182 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR G 61 " pdb=" OE1 GLU G 64 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR G 139 " pdb=" OG1 THR G 167 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR G 127 " pdb=" OE1 GLU G 185 " model vdw 2.250 3.040 nonbonded pdb=" OG SER H 2 " pdb=" O TYR H 41 " model vdw 2.266 3.040 ... (remaining 45335 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' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } 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: 1.180 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 0.054 5685 Z= 0.563 Angle : 0.803 7.684 7908 Z= 0.556 Chirality : 0.055 0.249 876 Planarity : 0.004 0.057 832 Dihedral : 20.302 159.238 2203 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.41 % Allowed : 9.80 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.26 (0.31), residues: 532 helix: -0.90 (0.30), residues: 222 sheet: -2.49 (0.42), residues: 102 loop : -1.40 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 242 TYR 0.024 0.002 TYR H 127 PHE 0.013 0.002 PHE H 190 TRP 0.015 0.002 TRP G 229 HIS 0.006 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.56 ( 5685) covalent geometry : angle 0.80318 / 0.56 ( 7908) hydrogen bonds : bond 0.12767 / 14.24 ( 308) hydrogen bonds : angle 6.31543 / 8.69 ( 884) *********************** 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 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.192 Fit side-chains REVERT: H 92 MET cc_start: 0.8306 (mmt) cc_final: 0.7896 (mmt) REVERT: H 259 MET cc_start: 0.8157 (ttp) cc_final: 0.7952 (ttm) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.1130 time to fit residues: 7.6088 Evaluate side-chains 38 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 42 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 45 GLN G 51 GLN G 76 HIS G 105 HIS G 148 GLN G 233 ASN H 3 GLN H 50 HIS H 154 ASN H 193 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087354 restraints weight = 8185.776| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.66 r_work: 0.3211 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5685 Z= 0.172 Angle : 0.581 7.983 7908 Z= 0.345 Chirality : 0.043 0.264 876 Planarity : 0.004 0.053 832 Dihedral : 22.360 159.530 1092 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 13.27 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.34), residues: 532 helix: 0.71 (0.33), residues: 228 sheet: -2.40 (0.48), residues: 90 loop : -1.21 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 220 TYR 0.020 0.002 TYR H 127 PHE 0.009 0.002 PHE H 190 TRP 0.014 0.001 TRP G 229 HIS 0.005 0.001 HIS H 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 5685) covalent geometry : angle 0.58058 / 0.35 ( 7908) hydrogen bonds : bond 0.04979 / 5.37 ( 308) hydrogen bonds : angle 4.78725 / 6.63 ( 884) *********************** 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: H 92 MET cc_start: 0.8691 (mmt) cc_final: 0.8195 (mmt) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.0775 time to fit residues: 5.2002 Evaluate side-chains 40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.102550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088345 restraints weight = 8197.753| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.68 r_work: 0.3228 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5685 Z= 0.146 Angle : 0.529 7.083 7908 Z= 0.320 Chirality : 0.042 0.285 876 Planarity : 0.004 0.051 832 Dihedral : 22.207 157.926 1090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.04 % Allowed : 15.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.36), residues: 532 helix: 1.33 (0.34), residues: 232 sheet: -2.16 (0.50), residues: 90 loop : -0.93 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 220 TYR 0.018 0.001 TYR H 127 PHE 0.007 0.001 PHE G 131 TRP 0.009 0.001 TRP G 229 HIS 0.003 0.001 HIS H 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 ( 5685) covalent geometry : angle 0.52898 / 0.32 ( 7908) hydrogen bonds : bond 0.04423 / 4.77 ( 308) hydrogen bonds : angle 4.51117 / 6.21 ( 884) *********************** 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 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: G 151 MET cc_start: 0.7975 (mmp) cc_final: 0.7550 (mmm) REVERT: G 264 PHE cc_start: 0.9125 (m-10) cc_final: 0.8922 (m-80) REVERT: H 92 MET cc_start: 0.8813 (mmt) cc_final: 0.8340 (mmt) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.0556 time to fit residues: 3.9328 Evaluate side-chains 42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089145 restraints weight = 8139.324| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.66 r_work: 0.3242 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5685 Z= 0.131 Angle : 0.505 6.966 7908 Z= 0.309 Chirality : 0.041 0.274 876 Planarity : 0.003 0.049 832 Dihedral : 22.141 157.191 1090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.84 % Allowed : 14.90 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.36), residues: 532 helix: 1.63 (0.33), residues: 232 sheet: -1.94 (0.52), residues: 90 loop : -0.74 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 12 TYR 0.017 0.001 TYR H 127 PHE 0.009 0.001 PHE G 264 TRP 0.008 0.001 TRP G 229 HIS 0.003 0.001 HIS H 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 5685) covalent geometry : angle 0.50522 / 0.31 ( 7908) hydrogen bonds : bond 0.04030 / 4.37 ( 308) hydrogen bonds : angle 4.26585 / 5.91 ( 884) *********************** 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: G 151 MET cc_start: 0.8035 (mmp) cc_final: 0.7628 (mmm) REVERT: G 264 PHE cc_start: 0.9050 (m-10) cc_final: 0.8821 (m-80) REVERT: H 84 GLU cc_start: 0.8051 (tt0) cc_final: 0.7845 (tt0) REVERT: H 92 MET cc_start: 0.8808 (mmt) cc_final: 0.8293 (mmt) REVERT: H 123 GLU cc_start: 0.8447 (pm20) cc_final: 0.8163 (pt0) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.0501 time to fit residues: 3.6816 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088796 restraints weight = 8198.012| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3240 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5685 Z= 0.143 Angle : 0.499 6.901 7908 Z= 0.306 Chirality : 0.041 0.282 876 Planarity : 0.003 0.047 832 Dihedral : 22.154 156.582 1090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.63 % Allowed : 15.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.36), residues: 532 helix: 1.76 (0.33), residues: 232 sheet: -1.76 (0.53), residues: 90 loop : -0.66 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 12 TYR 0.018 0.001 TYR H 127 PHE 0.007 0.001 PHE H 131 TRP 0.008 0.001 TRP H 229 HIS 0.003 0.001 HIS G 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 5685) covalent geometry : angle 0.49931 / 0.31 ( 7908) hydrogen bonds : bond 0.03991 / 4.32 ( 308) hydrogen bonds : angle 4.20676 / 5.79 ( 884) *********************** 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 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: H 92 MET cc_start: 0.8819 (mmt) cc_final: 0.8427 (mmt) outliers start: 8 outliers final: 8 residues processed: 46 average time/residue: 0.0539 time to fit residues: 3.8008 Evaluate side-chains 42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089348 restraints weight = 8177.588| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.68 r_work: 0.3244 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5685 Z= 0.135 Angle : 0.502 7.884 7908 Z= 0.304 Chirality : 0.040 0.276 876 Planarity : 0.003 0.047 832 Dihedral : 22.137 156.280 1090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.84 % Allowed : 15.10 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.36), residues: 532 helix: 1.92 (0.33), residues: 232 sheet: -1.64 (0.54), residues: 90 loop : -0.56 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.016 0.001 TYR H 127 PHE 0.012 0.001 PHE H 131 TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 5685) covalent geometry : angle 0.50158 / 0.30 ( 7908) hydrogen bonds : bond 0.03874 / 4.22 ( 308) hydrogen bonds : angle 4.13413 / 5.71 ( 884) *********************** 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 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: G 151 MET cc_start: 0.8233 (mmm) cc_final: 0.7896 (mmt) REVERT: H 92 MET cc_start: 0.8805 (mmt) cc_final: 0.8403 (mmt) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.0488 time to fit residues: 3.4324 Evaluate side-chains 41 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 HIS H 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089183 restraints weight = 8263.959| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.69 r_work: 0.3240 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5685 Z= 0.142 Angle : 0.495 6.465 7908 Z= 0.301 Chirality : 0.040 0.277 876 Planarity : 0.003 0.046 832 Dihedral : 22.153 156.003 1090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.24 % Allowed : 14.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.36), residues: 532 helix: 1.96 (0.33), residues: 232 sheet: -1.58 (0.53), residues: 90 loop : -0.49 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.018 0.001 TYR H 127 PHE 0.009 0.001 PHE H 131 TRP 0.008 0.001 TRP G 229 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 5685) covalent geometry : angle 0.49544 / 0.30 ( 7908) hydrogen bonds : bond 0.03861 / 4.22 ( 308) hydrogen bonds : angle 4.07284 / 5.65 ( 884) *********************** 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 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: H 92 MET cc_start: 0.8805 (mmt) cc_final: 0.8450 (mmt) outliers start: 11 outliers final: 10 residues processed: 46 average time/residue: 0.0503 time to fit residues: 3.6040 Evaluate side-chains 45 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.102782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088422 restraints weight = 8192.554| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.67 r_work: 0.3227 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5685 Z= 0.179 Angle : 0.527 10.739 7908 Z= 0.311 Chirality : 0.041 0.287 876 Planarity : 0.004 0.045 832 Dihedral : 22.218 155.883 1090 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.45 % Allowed : 15.71 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.36), residues: 532 helix: 1.98 (0.33), residues: 232 sheet: -1.44 (0.50), residues: 96 loop : -0.34 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.021 0.001 TYR H 127 PHE 0.009 0.001 PHE H 131 TRP 0.008 0.001 TRP G 229 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 ( 5685) covalent geometry : angle 0.52690 / 0.31 ( 7908) hydrogen bonds : bond 0.03954 / 4.33 ( 308) hydrogen bonds : angle 4.08489 / 5.66 ( 884) *********************** 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.193 Fit side-chains REVERT: G 151 MET cc_start: 0.8201 (mmm) cc_final: 0.7900 (mmt) REVERT: G 259 MET cc_start: 0.8497 (ttm) cc_final: 0.8289 (mtt) REVERT: H 92 MET cc_start: 0.8806 (mmt) cc_final: 0.8450 (mmt) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.0499 time to fit residues: 3.6629 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 44 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089742 restraints weight = 8205.495| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.68 r_work: 0.3254 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5685 Z= 0.130 Angle : 0.509 10.068 7908 Z= 0.302 Chirality : 0.040 0.269 876 Planarity : 0.003 0.046 832 Dihedral : 22.121 155.954 1090 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.84 % Allowed : 16.12 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.36), residues: 532 helix: 2.08 (0.33), residues: 232 sheet: -1.65 (0.52), residues: 94 loop : -0.51 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 242 TYR 0.015 0.001 TYR H 127 PHE 0.008 0.001 PHE H 131 TRP 0.010 0.001 TRP G 229 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 5685) covalent geometry : angle 0.50929 / 0.30 ( 7908) hydrogen bonds : bond 0.03759 / 4.10 ( 308) hydrogen bonds : angle 4.01959 / 5.60 ( 884) *********************** 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 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.203 Fit side-chains REVERT: G 151 MET cc_start: 0.8105 (mmm) cc_final: 0.7858 (mmt) REVERT: G 227 MET cc_start: 0.9096 (mmm) cc_final: 0.8888 (mmt) REVERT: G 259 MET cc_start: 0.8462 (ttm) cc_final: 0.8258 (mtt) REVERT: H 92 MET cc_start: 0.8790 (mmt) cc_final: 0.8437 (mmt) outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.0507 time to fit residues: 3.6941 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 128 SER 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 9 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.103405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089066 restraints weight = 8281.524| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.68 r_work: 0.3238 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5685 Z= 0.164 Angle : 0.539 10.525 7908 Z= 0.315 Chirality : 0.041 0.279 876 Planarity : 0.004 0.044 832 Dihedral : 22.162 155.626 1090 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.84 % Allowed : 16.73 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.36), residues: 532 helix: 2.11 (0.33), residues: 232 sheet: -1.68 (0.52), residues: 94 loop : -0.48 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 81 TYR 0.022 0.001 TYR G 216 PHE 0.008 0.001 PHE H 131 TRP 0.019 0.002 TRP G 258 HIS 0.014 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 5685) covalent geometry : angle 0.53931 / 0.31 ( 7908) hydrogen bonds : bond 0.03852 / 4.20 ( 308) hydrogen bonds : angle 4.02949 / 5.60 ( 884) ********************** 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 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.202 Fit side-chains REVERT: G 151 MET cc_start: 0.8080 (mmm) cc_final: 0.7857 (mmt) REVERT: G 227 MET cc_start: 0.9093 (mmm) cc_final: 0.8796 (mmm) REVERT: G 259 MET cc_start: 0.8484 (ttm) cc_final: 0.8274 (mtt) REVERT: H 92 MET cc_start: 0.8800 (mmt) cc_final: 0.8438 (mmt) outliers start: 9 outliers final: 9 residues processed: 43 average time/residue: 0.0508 time to fit residues: 3.4245 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 128 SER 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 7 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088270 restraints weight = 8497.059| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.68 r_work: 0.3233 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5685 Z= 0.189 Angle : 0.557 9.875 7908 Z= 0.324 Chirality : 0.041 0.294 876 Planarity : 0.004 0.043 832 Dihedral : 22.291 155.717 1090 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.45 % Allowed : 16.12 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.36), residues: 532 helix: 2.11 (0.33), residues: 232 sheet: -1.74 (0.52), residues: 94 loop : -0.52 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.021 0.001 TYR H 127 PHE 0.009 0.002 PHE G 7 TRP 0.030 0.002 TRP G 258 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 5685) covalent geometry : angle 0.55709 / 0.32 ( 7908) hydrogen bonds : bond 0.04050 / 4.45 ( 308) hydrogen bonds : angle 4.09169 / 5.69 ( 884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.70 seconds wall clock time: 24 minutes 40.83 seconds (1480.83 seconds total)