Starting phenix.real_space_refine on Tue Mar 3 14:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlk_22246/03_2026/6xlk_22246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlk_22246/03_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_22246/03_2026/6xlk_22246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlk_22246/03_2026/6xlk_22246.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlk_22246/03_2026/6xlk_22246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlk_22246/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 14 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: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.53, per 1000 atoms: 0.28 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: 0.53 Conformation dependent library (CDL) restraints added in 268.3 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, 28.2% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.75 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: 0.91 Time building geometry restraints manager: 0.68 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="SB 118 H 302 " pdb=" C1C 118 H 302 " ideal model delta sigma weight residual 2.092 2.132 -0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb="SB 118 G 302 " pdb=" C1C 118 G 302 " ideal model delta sigma weight residual 2.092 2.132 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb="SB 118 G 302 " pdb=" C1D 118 G 302 " ideal model delta sigma weight residual 2.092 2.129 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb="SB 118 H 302 " pdb=" C1D 118 H 302 " ideal model delta sigma weight residual 2.092 2.128 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.11e+00 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 7506 1.54 - 3.07: 348 3.07 - 4.61: 43 4.61 - 6.15: 6 6.15 - 7.68: 5 Bond angle restraints: 7908 Sorted by residual: angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.66 -4.46 1.50e+00 4.44e-01 8.85e+00 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 113.79 -3.09 1.22e+00 6.72e-01 6.44e+00 angle pdb=" CA TYR H 127 " pdb=" CB TYR H 127 " pdb=" CG TYR H 127 " ideal model delta sigma weight residual 113.90 118.39 -4.49 1.80e+00 3.09e-01 6.22e+00 angle pdb=" C4' DG T 40 " pdb=" O4' DG T 40 " pdb=" C1' DG T 40 " ideal model delta sigma weight residual 109.70 105.97 3.73 1.50e+00 4.44e-01 6.17e+00 angle pdb=" C THR G 206 " pdb=" CA THR G 206 " pdb=" CB THR G 206 " ideal model delta sigma weight residual 109.80 113.58 -3.78 1.64e+00 3.72e-01 5.31e+00 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.85: 3077 31.85 - 63.70: 276 63.70 - 95.54: 13 95.54 - 127.39: 2 127.39 - 159.24: 1 Dihedral angle restraints: 3369 sinusoidal: 1773 harmonic: 1596 Sorted by residual: dihedral pdb=" C23 1N7 H 301 " pdb=" C20 1N7 H 301 " pdb=" C22 1N7 H 301 " pdb=" C9 1N7 H 301 " ideal model delta sinusoidal sigma weight residual 155.16 -89.44 -115.40 1 3.00e+01 1.11e-03 1.52e+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 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 ... (remaining 3366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 639 0.050 - 0.100: 190 0.100 - 0.150: 36 0.150 - 0.199: 7 0.199 - 0.249: 4 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=" 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 chirality pdb=" C13 1N7 G 301 " pdb=" C12 1N7 G 301 " pdb=" C14 1N7 G 301 " pdb=" O2 1N7 G 301 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+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: 1.330 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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= 0.368 Angle : 0.756 7.684 7908 Z= 0.424 Chirality : 0.050 0.249 876 Planarity : 0.004 0.057 832 Dihedral : 20.173 159.238 2341 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 covalent geometry : bond 0.00823 ( 5685) covalent geometry : angle 0.75573 ( 7908) hydrogen bonds : bond 0.12767 ( 308) hydrogen bonds : angle 6.31543 ( 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 : 0.183 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: 0.1221 time to fit residues: 8.1202 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 : 0.198 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.102272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088060 restraints weight = 8222.062| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.66 r_work: 0.3226 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5685 Z= 0.163 Angle : 0.534 7.435 7908 Z= 0.305 Chirality : 0.040 0.217 876 Planarity : 0.004 0.053 832 Dihedral : 20.844 158.546 1230 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.45 % Allowed : 12.24 % Favored : 85.31 % 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: -0.81 (0.35), residues: 532 helix: 0.87 (0.34), residues: 232 sheet: -2.35 (0.48), residues: 90 loop : -1.19 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 12 TYR 0.018 0.001 TYR H 127 PHE 0.011 0.001 PHE H 190 TRP 0.012 0.001 TRP G 229 HIS 0.004 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5685) covalent geometry : angle 0.53384 ( 7908) hydrogen bonds : bond 0.04171 ( 308) hydrogen bonds : angle 4.48320 ( 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 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: G 259 MET cc_start: 0.8384 (ttm) cc_final: 0.8065 (ttm) REVERT: H 92 MET cc_start: 0.8681 (mmt) cc_final: 0.8205 (mmt) outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 0.0837 time to fit residues: 6.4228 Evaluate side-chains 41 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 233 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 = 0.3587 r_free = 0.3587 target = 0.102912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088582 restraints weight = 8206.680| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.67 r_work: 0.3226 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5685 Z= 0.170 Angle : 0.520 7.267 7908 Z= 0.296 Chirality : 0.039 0.150 876 Planarity : 0.004 0.050 832 Dihedral : 20.627 158.026 1228 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.04 % Allowed : 14.69 % 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: -0.15 (0.36), residues: 532 helix: 1.47 (0.34), residues: 232 sheet: -2.06 (0.50), residues: 90 loop : -0.90 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 12 TYR 0.018 0.001 TYR H 127 PHE 0.013 0.001 PHE G 264 TRP 0.008 0.001 TRP G 229 HIS 0.002 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5685) covalent geometry : angle 0.51982 ( 7908) hydrogen bonds : bond 0.03905 ( 308) hydrogen bonds : angle 4.28542 ( 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 : 0.205 Fit side-chains REVERT: G 227 MET cc_start: 0.8882 (mmm) cc_final: 0.8544 (mmm) REVERT: G 247 ASP cc_start: 0.8102 (m-30) cc_final: 0.7895 (m-30) REVERT: G 259 MET cc_start: 0.8371 (ttm) cc_final: 0.8045 (ttm) REVERT: H 92 MET cc_start: 0.8854 (mmt) cc_final: 0.8335 (mmt) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.0491 time to fit residues: 3.5454 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 184 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 31 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090427 restraints weight = 8172.639| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.63 r_work: 0.3261 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5685 Z= 0.132 Angle : 0.480 6.763 7908 Z= 0.277 Chirality : 0.038 0.148 876 Planarity : 0.003 0.048 832 Dihedral : 20.398 157.195 1228 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 14.49 % 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 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: 0.21 (0.36), residues: 532 helix: 1.91 (0.34), residues: 232 sheet: -2.05 (0.50), residues: 94 loop : -0.76 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 81 TYR 0.018 0.001 TYR H 127 PHE 0.009 0.001 PHE G 264 TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5685) covalent geometry : angle 0.48015 ( 7908) hydrogen bonds : bond 0.03533 ( 308) hydrogen bonds : angle 4.00696 ( 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 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.185 Fit side-chains REVERT: G 227 MET cc_start: 0.8822 (mmm) cc_final: 0.8596 (mmm) REVERT: H 92 MET cc_start: 0.8842 (mmt) cc_final: 0.8400 (mmt) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.0488 time to fit residues: 3.7184 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 184 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 Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089096 restraints weight = 8225.320| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.67 r_work: 0.3243 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5685 Z= 0.157 Angle : 0.499 7.637 7908 Z= 0.283 Chirality : 0.039 0.142 876 Planarity : 0.003 0.047 832 Dihedral : 20.452 156.925 1228 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.24 % Allowed : 15.51 % 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 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: 0.35 (0.36), residues: 532 helix: 2.00 (0.34), residues: 232 sheet: -1.96 (0.51), residues: 94 loop : -0.66 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.018 0.001 TYR H 127 PHE 0.009 0.001 PHE G 264 TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5685) covalent geometry : angle 0.49852 ( 7908) hydrogen bonds : bond 0.03582 ( 308) hydrogen bonds : angle 4.01256 ( 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.221 Fit side-chains REVERT: G 151 MET cc_start: 0.8275 (mmm) cc_final: 0.7792 (mmm) REVERT: G 259 MET cc_start: 0.8457 (ttm) cc_final: 0.8234 (mtt) REVERT: H 92 MET cc_start: 0.8818 (mmt) cc_final: 0.8478 (mmt) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.0475 time to fit residues: 3.6133 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 184 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 208 VAL Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090275 restraints weight = 8504.869| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.69 r_work: 0.3268 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.130 Angle : 0.484 7.772 7908 Z= 0.276 Chirality : 0.038 0.142 876 Planarity : 0.003 0.046 832 Dihedral : 20.351 156.697 1228 Min Nonbonded Distance : 2.594 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: 0.51 (0.37), residues: 532 helix: 2.16 (0.34), residues: 232 sheet: -1.89 (0.47), residues: 106 loop : -0.51 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.016 0.001 TYR H 127 PHE 0.009 0.001 PHE G 264 TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5685) covalent geometry : angle 0.48413 ( 7908) hydrogen bonds : bond 0.03384 ( 308) hydrogen bonds : angle 3.94582 ( 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.198 Fit side-chains REVERT: G 151 MET cc_start: 0.8161 (mmm) cc_final: 0.7801 (mmm) REVERT: G 227 MET cc_start: 0.8900 (mmm) cc_final: 0.8616 (mmm) REVERT: G 259 MET cc_start: 0.8445 (ttm) cc_final: 0.8235 (mtt) REVERT: H 92 MET cc_start: 0.8816 (mmt) cc_final: 0.8465 (mmt) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.0511 time to fit residues: 3.7903 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 184 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 208 VAL Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 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 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089792 restraints weight = 8516.176| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.69 r_work: 0.3256 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2221 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= 0.147 Angle : 0.483 8.329 7908 Z= 0.275 Chirality : 0.038 0.141 876 Planarity : 0.003 0.045 832 Dihedral : 20.391 156.590 1228 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.65 % Allowed : 16.12 % Favored : 81.22 % 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: 0.60 (0.37), residues: 532 helix: 2.19 (0.34), residues: 234 sheet: -1.84 (0.47), residues: 106 loop : -0.42 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.017 0.001 TYR H 127 PHE 0.010 0.001 PHE G 264 TRP 0.007 0.001 TRP H 229 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5685) covalent geometry : angle 0.48278 ( 7908) hydrogen bonds : bond 0.03443 ( 308) hydrogen bonds : angle 3.92848 ( 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.182 Fit side-chains REVERT: G 227 MET cc_start: 0.8900 (mmm) cc_final: 0.8584 (mmm) REVERT: G 259 MET cc_start: 0.8477 (ttm) cc_final: 0.8274 (mtt) REVERT: H 92 MET cc_start: 0.8814 (mmt) cc_final: 0.8512 (mmt) outliers start: 13 outliers final: 12 residues processed: 50 average time/residue: 0.0452 time to fit residues: 3.5025 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 : 0.179 ------------------------------------------------------------------------------- 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 184 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 160 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.104763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090321 restraints weight = 8396.724| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.67 r_work: 0.3268 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2279 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= 0.133 Angle : 0.496 11.027 7908 Z= 0.277 Chirality : 0.038 0.157 876 Planarity : 0.003 0.045 832 Dihedral : 20.354 156.565 1228 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.45 % Allowed : 16.73 % Favored : 80.82 % 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: 0.70 (0.37), residues: 532 helix: 2.26 (0.34), residues: 234 sheet: -1.78 (0.47), residues: 106 loop : -0.36 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.016 0.001 TYR H 127 PHE 0.009 0.001 PHE G 264 TRP 0.008 0.001 TRP H 229 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5685) covalent geometry : angle 0.49641 ( 7908) hydrogen bonds : bond 0.03375 ( 308) hydrogen bonds : angle 3.90701 ( 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.184 Fit side-chains REVERT: G 151 MET cc_start: 0.8197 (mmm) cc_final: 0.7938 (mmt) REVERT: G 227 MET cc_start: 0.8898 (mmm) cc_final: 0.8573 (mmm) REVERT: G 259 MET cc_start: 0.8472 (ttm) cc_final: 0.8263 (mtt) REVERT: H 92 MET cc_start: 0.8803 (mmt) cc_final: 0.8493 (mmt) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.0462 time to fit residues: 3.4901 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 184 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 208 VAL Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090548 restraints weight = 8503.509| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.69 r_work: 0.3272 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2329 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= 0.133 Angle : 0.494 10.020 7908 Z= 0.276 Chirality : 0.038 0.154 876 Planarity : 0.003 0.044 832 Dihedral : 20.332 156.453 1228 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.06 % Allowed : 16.12 % Favored : 80.82 % 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: 0.77 (0.37), residues: 532 helix: 2.32 (0.34), residues: 234 sheet: -1.74 (0.48), residues: 106 loop : -0.31 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.016 0.001 TYR H 127 PHE 0.009 0.001 PHE G 264 TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5685) covalent geometry : angle 0.49377 ( 7908) hydrogen bonds : bond 0.03357 ( 308) hydrogen bonds : angle 3.89095 ( 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.156 Fit side-chains REVERT: G 151 MET cc_start: 0.8164 (mmm) cc_final: 0.7916 (mmt) REVERT: G 227 MET cc_start: 0.8884 (mmm) cc_final: 0.8558 (mmm) REVERT: G 259 MET cc_start: 0.8489 (ttm) cc_final: 0.8278 (mtt) REVERT: H 92 MET cc_start: 0.8800 (mmt) cc_final: 0.8491 (mmt) outliers start: 15 outliers final: 13 residues processed: 50 average time/residue: 0.0475 time to fit residues: 3.6698 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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 184 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 146 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.104138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089596 restraints weight = 8449.796| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.68 r_work: 0.3253 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5685 Z= 0.168 Angle : 0.514 10.417 7908 Z= 0.286 Chirality : 0.039 0.152 876 Planarity : 0.004 0.043 832 Dihedral : 20.421 156.605 1228 Min Nonbonded Distance : 2.593 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: 0.80 (0.37), residues: 532 helix: 2.28 (0.33), residues: 234 sheet: -1.67 (0.52), residues: 94 loop : -0.37 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.019 0.001 TYR H 127 PHE 0.011 0.001 PHE G 264 TRP 0.007 0.001 TRP H 229 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5685) covalent geometry : angle 0.51354 ( 7908) hydrogen bonds : bond 0.03495 ( 308) hydrogen bonds : angle 3.94955 ( 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.141 Fit side-chains REVERT: G 151 MET cc_start: 0.8182 (mmm) cc_final: 0.7948 (mmt) REVERT: G 259 MET cc_start: 0.8433 (ttm) cc_final: 0.8213 (mtt) REVERT: H 92 MET cc_start: 0.8812 (mmt) cc_final: 0.8506 (mmt) outliers start: 12 outliers final: 12 residues processed: 47 average time/residue: 0.0427 time to fit residues: 3.1984 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 : 0.200 ------------------------------------------------------------------------------- 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 184 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 146 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090515 restraints weight = 8414.815| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.68 r_work: 0.3269 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.139 Angle : 0.499 10.631 7908 Z= 0.279 Chirality : 0.038 0.153 876 Planarity : 0.003 0.044 832 Dihedral : 20.346 156.642 1228 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 15.92 % 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: 0.80 (0.37), residues: 532 helix: 2.34 (0.33), residues: 234 sheet: -1.71 (0.48), residues: 106 loop : -0.30 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 81 TYR 0.016 0.001 TYR H 127 PHE 0.007 0.001 PHE H 183 TRP 0.008 0.001 TRP G 229 HIS 0.001 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5685) covalent geometry : angle 0.49926 ( 7908) hydrogen bonds : bond 0.03367 ( 308) hydrogen bonds : angle 3.92849 ( 884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.32 seconds wall clock time: 24 minutes 22.15 seconds (1462.15 seconds total)