Starting phenix.real_space_refine on Thu Mar 6 09:54:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlk_22246/03_2025/6xlk_22246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlk_22246/03_2025/6xlk_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_2025/6xlk_22246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlk_22246/03_2025/6xlk_22246.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlk_22246/03_2025/6xlk_22246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlk_22246/03_2025/6xlk_22246.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.51, per 1000 atoms: 0.83 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: 1.82 Conformation dependent library (CDL) restraints added in 703.8 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: 2.01 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: 1.85 Time building geometry restraints manager: 1.72 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- 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= 0.504 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (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 TRP 0.015 0.002 TRP G 229 HIS 0.006 0.001 HIS G 105 PHE 0.013 0.002 PHE H 190 TYR 0.024 0.002 TYR H 127 ARG 0.005 0.001 ARG G 242 *********************** 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 : 0.563 Fit side-chains REVERT: H 92 MET cc_start: 0.8307 (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: 0.2725 time to fit residues: 18.2964 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 : 0.559 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.102477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088281 restraints weight = 8200.528| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.66 r_work: 0.3230 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5685 Z= 0.199 Angle : 0.530 7.405 7908 Z= 0.304 Chirality : 0.040 0.199 876 Planarity : 0.004 0.053 832 Dihedral : 20.822 158.435 1230 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.24 % Allowed : 12.24 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.35), residues: 532 helix: 0.86 (0.34), residues: 232 sheet: -2.36 (0.48), residues: 90 loop : -1.19 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 229 HIS 0.004 0.001 HIS H 170 PHE 0.010 0.001 PHE H 190 TYR 0.017 0.001 TYR H 127 ARG 0.005 0.001 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: G 259 MET cc_start: 0.8379 (ttm) cc_final: 0.8037 (ttm) REVERT: H 92 MET cc_start: 0.8680 (mmt) cc_final: 0.8207 (mmt) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.1897 time to fit residues: 14.3783 Evaluate side-chains 41 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088979 restraints weight = 8298.585| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.69 r_work: 0.3231 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1698 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= 0.214 Angle : 0.513 7.208 7908 Z= 0.292 Chirality : 0.039 0.146 876 Planarity : 0.003 0.050 832 Dihedral : 20.573 157.824 1228 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 : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.36), residues: 532 helix: 1.50 (0.34), residues: 232 sheet: -2.06 (0.50), residues: 90 loop : -0.87 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 229 HIS 0.002 0.001 HIS H 170 PHE 0.014 0.001 PHE G 264 TYR 0.017 0.001 TYR H 127 ARG 0.004 0.000 ARG H 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.554 Fit side-chains REVERT: G 227 MET cc_start: 0.8894 (mmm) cc_final: 0.8527 (mmm) REVERT: G 247 ASP cc_start: 0.8156 (m-30) cc_final: 0.7947 (m-30) REVERT: G 259 MET cc_start: 0.8393 (ttm) cc_final: 0.8061 (ttm) REVERT: H 92 MET cc_start: 0.8810 (mmt) cc_final: 0.8288 (mmt) REVERT: H 123 GLU cc_start: 0.8509 (pm20) cc_final: 0.8273 (pt0) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1412 time to fit residues: 10.0464 Evaluate side-chains 45 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.104988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090562 restraints weight = 8431.432| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.71 r_work: 0.3259 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2055 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= 0.166 Angle : 0.476 6.834 7908 Z= 0.275 Chirality : 0.038 0.146 876 Planarity : 0.003 0.049 832 Dihedral : 20.366 157.033 1228 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.84 % Allowed : 14.69 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.36), residues: 532 helix: 1.89 (0.33), residues: 232 sheet: -1.92 (0.47), residues: 102 loop : -0.59 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS H 212 PHE 0.009 0.001 PHE H 131 TYR 0.017 0.001 TYR H 127 ARG 0.003 0.000 ARG H 12 *********************** 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.630 Fit side-chains REVERT: G 227 MET cc_start: 0.8868 (mmm) cc_final: 0.8639 (mmm) REVERT: G 247 ASP cc_start: 0.8109 (m-30) cc_final: 0.7865 (m-30) REVERT: G 259 MET cc_start: 0.8390 (ttm) cc_final: 0.8170 (ttm) REVERT: H 92 MET cc_start: 0.8846 (mmt) cc_final: 0.8408 (mmt) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1237 time to fit residues: 9.0441 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 : 0.622 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.0010 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.103738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089473 restraints weight = 8138.130| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.65 r_work: 0.3250 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2103 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= 0.200 Angle : 0.499 7.590 7908 Z= 0.283 Chirality : 0.039 0.153 876 Planarity : 0.003 0.047 832 Dihedral : 20.413 156.750 1228 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.63 % Allowed : 15.51 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.36), residues: 532 helix: 2.02 (0.34), residues: 232 sheet: -1.96 (0.47), residues: 106 loop : -0.60 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 229 HIS 0.005 0.001 HIS G 105 PHE 0.009 0.001 PHE G 264 TYR 0.018 0.001 TYR H 127 ARG 0.003 0.000 ARG H 81 *********************** 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 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.875 Fit side-chains REVERT: G 151 MET cc_start: 0.8232 (mmm) cc_final: 0.7734 (mmm) REVERT: H 92 MET cc_start: 0.8815 (mmt) cc_final: 0.8472 (mmt) REVERT: H 123 GLU cc_start: 0.8505 (pm20) cc_final: 0.8284 (pt0) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.1546 time to fit residues: 10.0438 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.106109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091747 restraints weight = 8355.225| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.68 r_work: 0.3287 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2345 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= 0.155 Angle : 0.476 7.686 7908 Z= 0.272 Chirality : 0.038 0.152 876 Planarity : 0.003 0.046 832 Dihedral : 20.267 156.283 1228 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 15.51 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.37), residues: 532 helix: 2.12 (0.34), residues: 234 sheet: -1.88 (0.48), residues: 106 loop : -0.44 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 229 HIS 0.002 0.001 HIS H 212 PHE 0.009 0.001 PHE G 264 TYR 0.015 0.001 TYR H 127 ARG 0.002 0.000 ARG H 81 *********************** 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: 10 poor density : 40 time to evaluate : 0.729 Fit side-chains REVERT: G 150 VAL cc_start: 0.8993 (p) cc_final: 0.8736 (p) REVERT: G 227 MET cc_start: 0.8882 (mmm) cc_final: 0.8614 (mmm) REVERT: H 92 MET cc_start: 0.8807 (mmt) cc_final: 0.8510 (mmt) outliers start: 10 outliers final: 9 residues processed: 49 average time/residue: 0.1479 time to fit residues: 10.5671 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 : 0.855 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3621 r_free = 0.3621 target = 0.104954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090578 restraints weight = 8299.714| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.66 r_work: 0.3274 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2340 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= 0.188 Angle : 0.489 8.719 7908 Z= 0.276 Chirality : 0.038 0.148 876 Planarity : 0.003 0.045 832 Dihedral : 20.329 156.201 1228 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.24 % Allowed : 16.12 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.37), residues: 532 helix: 2.18 (0.34), residues: 234 sheet: -1.80 (0.48), residues: 106 loop : -0.42 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 258 HIS 0.005 0.001 HIS G 105 PHE 0.008 0.001 PHE H 131 TYR 0.017 0.001 TYR H 127 ARG 0.002 0.000 ARG H 81 *********************** 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 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.596 Fit side-chains REVERT: G 150 VAL cc_start: 0.9021 (p) cc_final: 0.8773 (p) REVERT: G 151 MET cc_start: 0.8372 (mmm) cc_final: 0.7878 (mmt) REVERT: G 227 MET cc_start: 0.8879 (mmm) cc_final: 0.8584 (mmm) REVERT: H 92 MET cc_start: 0.8818 (mmt) cc_final: 0.8537 (mmt) outliers start: 11 outliers final: 10 residues processed: 46 average time/residue: 0.1559 time to fit residues: 11.0113 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 198 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.104746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090384 restraints weight = 8265.199| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.66 r_work: 0.3270 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2342 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= 0.195 Angle : 0.491 9.196 7908 Z= 0.276 Chirality : 0.038 0.146 876 Planarity : 0.003 0.044 832 Dihedral : 20.357 156.286 1228 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.37), residues: 532 helix: 2.19 (0.34), residues: 234 sheet: -1.77 (0.48), residues: 106 loop : -0.33 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 258 HIS 0.006 0.001 HIS G 105 PHE 0.010 0.001 PHE G 264 TYR 0.017 0.001 TYR H 127 ARG 0.002 0.000 ARG H 81 *********************** 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.529 Fit side-chains REVERT: G 150 VAL cc_start: 0.9035 (p) cc_final: 0.8805 (p) REVERT: G 151 MET cc_start: 0.8271 (mmm) cc_final: 0.7791 (mmt) REVERT: G 227 MET cc_start: 0.8881 (mmm) cc_final: 0.8559 (mmm) REVERT: H 92 MET cc_start: 0.8840 (mmt) cc_final: 0.8547 (mmt) outliers start: 13 outliers final: 12 residues processed: 48 average time/residue: 0.1212 time to fit residues: 8.8247 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 198 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.105410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091083 restraints weight = 8233.432| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.65 r_work: 0.3282 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2421 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= 0.167 Angle : 0.484 10.183 7908 Z= 0.273 Chirality : 0.038 0.147 876 Planarity : 0.003 0.045 832 Dihedral : 20.303 156.227 1228 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.45 % Allowed : 16.53 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.37), residues: 532 helix: 2.25 (0.34), residues: 234 sheet: -1.75 (0.48), residues: 106 loop : -0.28 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 258 HIS 0.003 0.001 HIS G 105 PHE 0.009 0.001 PHE G 264 TYR 0.015 0.001 TYR H 127 ARG 0.002 0.000 ARG H 81 *********************** 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.562 Fit side-chains REVERT: G 150 VAL cc_start: 0.9036 (p) cc_final: 0.8819 (p) REVERT: G 151 MET cc_start: 0.8298 (mmm) cc_final: 0.7809 (mmt) REVERT: G 227 MET cc_start: 0.8867 (mmm) cc_final: 0.8537 (mmm) REVERT: H 47 MET cc_start: 0.8926 (ttp) cc_final: 0.8720 (ttp) REVERT: H 92 MET cc_start: 0.8826 (mmt) cc_final: 0.8534 (mmt) outliers start: 12 outliers final: 11 residues processed: 47 average time/residue: 0.1472 time to fit residues: 10.4357 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.105918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091485 restraints weight = 8254.604| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.66 r_work: 0.3282 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2449 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= 0.175 Angle : 0.486 10.636 7908 Z= 0.274 Chirality : 0.038 0.147 876 Planarity : 0.003 0.045 832 Dihedral : 20.298 156.072 1228 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.45 % Allowed : 16.53 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 532 helix: 2.28 (0.34), residues: 234 sheet: -1.75 (0.48), residues: 106 loop : -0.26 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 258 HIS 0.004 0.001 HIS G 105 PHE 0.009 0.001 PHE G 264 TYR 0.016 0.001 TYR H 127 ARG 0.002 0.000 ARG H 242 ********************** 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 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.566 Fit side-chains REVERT: G 151 MET cc_start: 0.8311 (mmm) cc_final: 0.7814 (mmt) REVERT: G 227 MET cc_start: 0.8873 (mmm) cc_final: 0.8539 (mmm) REVERT: H 47 MET cc_start: 0.8950 (ttp) cc_final: 0.8745 (ttp) REVERT: H 92 MET cc_start: 0.8812 (mmt) cc_final: 0.8518 (mmt) outliers start: 12 outliers final: 11 residues processed: 46 average time/residue: 0.1171 time to fit residues: 8.2303 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 128 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 5 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS H 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091634 restraints weight = 8264.591| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.65 r_work: 0.3291 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2545 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= 0.167 Angle : 0.482 10.883 7908 Z= 0.272 Chirality : 0.038 0.146 876 Planarity : 0.003 0.045 832 Dihedral : 20.259 155.888 1228 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.45 % Allowed : 16.53 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.37), residues: 532 helix: 2.32 (0.34), residues: 234 sheet: -1.70 (0.48), residues: 106 loop : -0.24 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 258 HIS 0.002 0.001 HIS G 105 PHE 0.008 0.001 PHE G 264 TYR 0.015 0.001 TYR H 127 ARG 0.002 0.000 ARG H 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.70 seconds wall clock time: 59 minutes 8.03 seconds (3548.03 seconds total)