Starting phenix.real_space_refine on Wed Mar 5 23:25:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wfq_21652/03_2025/6wfq_21652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wfq_21652/03_2025/6wfq_21652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2025/6wfq_21652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2025/6wfq_21652.map" model { file = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2025/6wfq_21652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wfq_21652/03_2025/6wfq_21652.cif" } resolution = 3.9 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= 0.002 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 10 5.16 5 C 2508 2.51 5 N 769 2.21 5 O 847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 4164 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1812 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "D" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1737 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain: "A" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Time building chain proxies: 3.18, per 1000 atoms: 0.76 Number of scatterers: 4164 At special positions: 0 Unit cell: (80.24, 99.96, 82.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 30 15.00 O 847 8.00 N 769 7.00 C 2508 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: 1.07 Conformation dependent library (CDL) restraints added in 412.3 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 75.2% alpha, 0.0% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'C' and resid 31 through 46 removed outlier: 4.013A pdb=" N MET C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 68 through 83 removed outlier: 3.714A pdb=" N VAL C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.585A pdb=" N ILE C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.691A pdb=" N PHE C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 142 Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.130A pdb=" N LEU C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 181 removed outlier: 4.326A pdb=" N ILE C 169 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 210 through 232 Processing helix chain 'C' and resid 233 through 248 removed outlier: 3.782A pdb=" N ALA C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.956A pdb=" N MET D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 3.671A pdb=" N VAL D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.795A pdb=" N ILE D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.785A pdb=" N HIS D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.984A pdb=" N HIS D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 removed outlier: 3.996A pdb=" N LEU D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 185 through 203 Processing helix chain 'D' and resid 208 through 231 removed outlier: 3.621A pdb=" N GLU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.803A pdb=" N ALA D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 248 " --> pdb=" O HIS D 244 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1063 1.33 - 1.45: 878 1.45 - 1.57: 2281 1.57 - 1.69: 58 1.69 - 1.80: 20 Bond restraints: 4300 Sorted by residual: bond pdb=" CB PRO D 204 " pdb=" CG PRO D 204 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.61e-01 bond pdb=" CA LYS C 31 " pdb=" C LYS C 31 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.34e-02 5.57e+03 5.46e-01 bond pdb=" C2' DT A 3 " pdb=" C1' DT A 3 " ideal model delta sigma weight residual 1.525 1.537 -0.012 2.00e-02 2.50e+03 3.75e-01 bond pdb=" C ARG D 97 " pdb=" N PRO D 98 " ideal model delta sigma weight residual 1.331 1.338 -0.008 1.31e-02 5.83e+03 3.38e-01 bond pdb=" C ILE C 182 " pdb=" N PRO C 183 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.30e-02 5.92e+03 3.33e-01 ... (remaining 4295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 5762 1.27 - 2.54: 141 2.54 - 3.81: 22 3.81 - 5.08: 7 5.08 - 6.35: 3 Bond angle restraints: 5935 Sorted by residual: angle pdb=" N LYS D 112 " pdb=" CA LYS D 112 " pdb=" C LYS D 112 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" CA LYS D 112 " pdb=" C LYS D 112 " pdb=" N ASP D 113 " ideal model delta sigma weight residual 119.71 116.95 2.76 1.17e+00 7.31e-01 5.57e+00 angle pdb=" N LYS C 82 " pdb=" CA LYS C 82 " pdb=" C LYS C 82 " ideal model delta sigma weight residual 112.54 109.84 2.70 1.22e+00 6.72e-01 4.90e+00 angle pdb=" N SER D 33 " pdb=" CA SER D 33 " pdb=" C SER D 33 " ideal model delta sigma weight residual 111.37 114.89 -3.52 1.65e+00 3.67e-01 4.55e+00 angle pdb=" O HIS C 244 " pdb=" C HIS C 244 " pdb=" N LEU C 245 " ideal model delta sigma weight residual 122.15 119.88 2.27 1.14e+00 7.69e-01 3.97e+00 ... (remaining 5930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 2176 16.59 - 33.17: 233 33.17 - 49.76: 106 49.76 - 66.34: 37 66.34 - 82.93: 2 Dihedral angle restraints: 2554 sinusoidal: 1251 harmonic: 1303 Sorted by residual: dihedral pdb=" N LEU C 79 " pdb=" CA LEU C 79 " pdb=" CB LEU C 79 " pdb=" CG LEU C 79 " ideal model delta sinusoidal sigma weight residual -60.00 -119.66 59.66 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS C 82 " pdb=" CB LYS C 82 " pdb=" CG LYS C 82 " pdb=" CD LYS C 82 " ideal model delta sinusoidal sigma weight residual 180.00 121.92 58.08 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB LYS C 82 " pdb=" CG LYS C 82 " pdb=" CD LYS C 82 " pdb=" CE LYS C 82 " ideal model delta sinusoidal sigma weight residual -60.00 -2.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 402 0.023 - 0.045: 161 0.045 - 0.068: 68 0.068 - 0.090: 16 0.090 - 0.113: 12 Chirality restraints: 659 Sorted by residual: chirality pdb=" CA ILE D 87 " pdb=" N ILE D 87 " pdb=" C ILE D 87 " pdb=" CB ILE D 87 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA PRO C 118 " pdb=" N PRO C 118 " pdb=" C PRO C 118 " pdb=" CB PRO C 118 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.76e-01 ... (remaining 656 not shown) Planarity restraints: 686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 244 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C HIS C 244 " 0.079 2.00e-02 2.50e+03 pdb=" O HIS C 244 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU C 245 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 244 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C HIS D 244 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS D 244 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D 245 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 69 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.92e-01 pdb=" N PRO C 70 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.012 5.00e-02 4.00e+02 ... (remaining 683 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 941 2.79 - 3.32: 4114 3.32 - 3.85: 7107 3.85 - 4.37: 7847 4.37 - 4.90: 12239 Nonbonded interactions: 32248 Sorted by model distance: nonbonded pdb=" O PHE D 131 " pdb=" OG SER D 134 " model vdw 2.265 3.040 nonbonded pdb=" O LEU D 211 " pdb=" ND2 ASN D 215 " model vdw 2.360 3.120 nonbonded pdb=" O SER C 99 " pdb=" OG1 THR C 102 " model vdw 2.390 3.040 nonbonded pdb=" O ASN D 158 " pdb=" OG SER D 161 " model vdw 2.399 3.040 nonbonded pdb=" O GLU C 156 " pdb=" OG SER C 159 " model vdw 2.399 3.040 ... (remaining 32243 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 'C' and resid 30 through 248) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.002 0.044 4300 Z= 0.118 Angle : 0.487 6.347 5935 Z= 0.295 Chirality : 0.032 0.113 659 Planarity : 0.003 0.045 686 Dihedral : 16.898 82.929 1700 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.80 % Allowed : 5.32 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.49 (0.35), residues: 443 helix: -0.75 (0.26), residues: 316 sheet: None (None), residues: 0 loop : -3.85 (0.44), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 198 HIS 0.004 0.000 HIS C 117 PHE 0.003 0.000 PHE C 131 TYR 0.014 0.001 TYR D 219 ARG 0.001 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 GLN cc_start: 0.9374 (tt0) cc_final: 0.8509 (tp40) REVERT: C 130 PHE cc_start: 0.9371 (m-10) cc_final: 0.8486 (m-80) REVERT: C 138 TYR cc_start: 0.8711 (t80) cc_final: 0.8335 (t80) REVERT: C 153 LYS cc_start: 0.9737 (pptt) cc_final: 0.9444 (tppt) REVERT: C 157 ILE cc_start: 0.9453 (tp) cc_final: 0.9055 (tp) REVERT: C 196 LEU cc_start: 0.9633 (mm) cc_final: 0.9379 (pp) REVERT: C 212 HIS cc_start: 0.9478 (p-80) cc_final: 0.9228 (m-70) REVERT: D 89 ASN cc_start: 0.8707 (t0) cc_final: 0.8426 (m-40) REVERT: D 135 LEU cc_start: 0.8854 (mt) cc_final: 0.8618 (mt) REVERT: D 147 GLN cc_start: 0.9042 (mp10) cc_final: 0.8619 (mp10) outliers start: 3 outliers final: 0 residues processed: 122 average time/residue: 0.1663 time to fit residues: 24.9012 Evaluate side-chains 74 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN D 192 HIS D 214 HIS D 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.069011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048156 restraints weight = 21113.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.049824 restraints weight = 14432.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051074 restraints weight = 11159.877| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4300 Z= 0.181 Angle : 0.661 10.573 5935 Z= 0.334 Chirality : 0.038 0.188 659 Planarity : 0.004 0.027 686 Dihedral : 18.334 59.660 822 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.33 % Allowed : 15.96 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.39), residues: 443 helix: 0.54 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -3.52 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 198 HIS 0.004 0.001 HIS C 117 PHE 0.010 0.001 PHE D 65 TYR 0.022 0.003 TYR C 219 ARG 0.003 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 GLN cc_start: 0.8853 (pt0) cc_final: 0.8370 (pt0) REVERT: C 101 ASP cc_start: 0.9609 (t0) cc_final: 0.9408 (p0) REVERT: C 126 GLN cc_start: 0.9461 (tt0) cc_final: 0.8909 (tp40) REVERT: C 138 TYR cc_start: 0.8774 (t80) cc_final: 0.8280 (t80) REVERT: C 153 LYS cc_start: 0.9755 (pptt) cc_final: 0.9510 (tptt) REVERT: C 212 HIS cc_start: 0.9424 (p-80) cc_final: 0.9212 (m-70) REVERT: D 35 MET cc_start: 0.9576 (tmm) cc_final: 0.9280 (ppp) REVERT: D 89 ASN cc_start: 0.8799 (t0) cc_final: 0.8557 (m-40) REVERT: D 97 ARG cc_start: 0.8892 (mmp80) cc_final: 0.8205 (mmp80) REVERT: D 147 GLN cc_start: 0.8986 (mp10) cc_final: 0.8591 (mp10) outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 0.1637 time to fit residues: 17.2868 Evaluate side-chains 81 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN D 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.069044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048555 restraints weight = 20192.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.050217 restraints weight = 13626.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.051444 restraints weight = 10467.638| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4300 Z= 0.173 Angle : 0.655 10.312 5935 Z= 0.328 Chirality : 0.038 0.136 659 Planarity : 0.003 0.036 686 Dihedral : 18.353 59.714 822 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.86 % Allowed : 15.16 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.39), residues: 443 helix: 0.76 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.33 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 198 HIS 0.005 0.001 HIS C 117 PHE 0.016 0.001 PHE D 114 TYR 0.015 0.002 TYR D 219 ARG 0.003 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.9436 (mp0) cc_final: 0.9231 (mp0) REVERT: C 42 GLN cc_start: 0.8871 (pt0) cc_final: 0.8656 (pt0) REVERT: C 43 MET cc_start: 0.9299 (mmm) cc_final: 0.9053 (mmm) REVERT: C 62 MET cc_start: 0.8499 (ttp) cc_final: 0.8150 (mtt) REVERT: C 101 ASP cc_start: 0.9613 (t0) cc_final: 0.9412 (p0) REVERT: C 126 GLN cc_start: 0.9447 (tt0) cc_final: 0.8634 (tp40) REVERT: C 130 PHE cc_start: 0.9415 (m-10) cc_final: 0.8611 (m-80) REVERT: C 138 TYR cc_start: 0.8746 (t80) cc_final: 0.8245 (t80) REVERT: C 153 LYS cc_start: 0.9741 (pptt) cc_final: 0.9481 (tptt) REVERT: C 157 ILE cc_start: 0.9428 (tp) cc_final: 0.9071 (tp) REVERT: C 212 HIS cc_start: 0.9422 (p-80) cc_final: 0.9191 (m-70) REVERT: D 35 MET cc_start: 0.9603 (tmm) cc_final: 0.9351 (ppp) REVERT: D 38 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9061 (mm-30) REVERT: D 62 MET cc_start: 0.1681 (ttt) cc_final: 0.1088 (tpp) REVERT: D 97 ARG cc_start: 0.8942 (mmp80) cc_final: 0.8306 (mmp80) REVERT: D 110 MET cc_start: 0.8082 (tpt) cc_final: 0.7667 (tpt) REVERT: D 147 GLN cc_start: 0.8935 (mp10) cc_final: 0.8525 (mp10) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 0.1705 time to fit residues: 18.1375 Evaluate side-chains 82 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 242 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.065982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.045889 restraints weight = 20811.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.047495 restraints weight = 13905.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048660 restraints weight = 10639.941| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4300 Z= 0.212 Angle : 0.672 10.267 5935 Z= 0.347 Chirality : 0.039 0.174 659 Planarity : 0.004 0.034 686 Dihedral : 18.521 59.512 822 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.46 % Allowed : 17.29 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.39), residues: 443 helix: 0.81 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -3.10 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 198 HIS 0.006 0.001 HIS D 192 PHE 0.011 0.001 PHE D 175 TYR 0.019 0.003 TYR D 219 ARG 0.005 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9545 (tmm) cc_final: 0.9135 (ppp) REVERT: C 42 GLN cc_start: 0.8909 (pt0) cc_final: 0.8630 (pt0) REVERT: C 43 MET cc_start: 0.9387 (mmm) cc_final: 0.9119 (mmm) REVERT: C 62 MET cc_start: 0.8521 (ttp) cc_final: 0.8157 (mtt) REVERT: C 101 ASP cc_start: 0.9610 (t0) cc_final: 0.9405 (p0) REVERT: C 126 GLN cc_start: 0.9450 (tt0) cc_final: 0.8741 (tp40) REVERT: C 130 PHE cc_start: 0.9478 (m-10) cc_final: 0.8846 (m-80) REVERT: C 181 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8732 (mt-10) REVERT: C 212 HIS cc_start: 0.9444 (p-80) cc_final: 0.9163 (m-70) REVERT: D 35 MET cc_start: 0.9626 (tmm) cc_final: 0.9424 (ppp) REVERT: D 38 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9059 (mm-30) REVERT: D 89 ASN cc_start: 0.8221 (m-40) cc_final: 0.8003 (m-40) REVERT: D 110 MET cc_start: 0.8066 (tpt) cc_final: 0.7677 (tpt) REVERT: D 147 GLN cc_start: 0.9001 (mp10) cc_final: 0.8584 (mp10) REVERT: D 221 GLN cc_start: 0.9071 (mt0) cc_final: 0.8665 (mt0) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1779 time to fit residues: 19.1814 Evaluate side-chains 84 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 40 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.067421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.047246 restraints weight = 20556.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048876 restraints weight = 13755.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.050046 restraints weight = 10511.197| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4300 Z= 0.179 Angle : 0.707 12.697 5935 Z= 0.349 Chirality : 0.039 0.141 659 Planarity : 0.003 0.033 686 Dihedral : 18.591 59.017 822 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.39 % Allowed : 21.54 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.40), residues: 443 helix: 0.88 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.90 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 198 HIS 0.011 0.001 HIS D 192 PHE 0.013 0.001 PHE D 175 TYR 0.018 0.002 TYR D 219 ARG 0.002 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.9584 (pp20) cc_final: 0.9349 (pp20) REVERT: C 42 GLN cc_start: 0.8888 (pt0) cc_final: 0.8567 (pt0) REVERT: C 43 MET cc_start: 0.9414 (mmm) cc_final: 0.9111 (mmm) REVERT: C 101 ASP cc_start: 0.9622 (t0) cc_final: 0.9412 (p0) REVERT: C 126 GLN cc_start: 0.9421 (tt0) cc_final: 0.8712 (tp40) REVERT: C 130 PHE cc_start: 0.9456 (m-10) cc_final: 0.8771 (m-80) REVERT: C 181 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8738 (mt-10) REVERT: D 38 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9068 (mm-30) REVERT: D 62 MET cc_start: 0.1501 (ttt) cc_final: 0.1081 (tpp) REVERT: D 97 ARG cc_start: 0.8853 (mmp80) cc_final: 0.8158 (mmp80) REVERT: D 110 MET cc_start: 0.7934 (tpt) cc_final: 0.7557 (tpt) REVERT: D 147 GLN cc_start: 0.8937 (mp10) cc_final: 0.8527 (mp10) REVERT: D 188 PHE cc_start: 0.9426 (m-80) cc_final: 0.9111 (m-80) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.1988 time to fit residues: 19.9731 Evaluate side-chains 79 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.067688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047509 restraints weight = 19865.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049154 restraints weight = 13534.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.050363 restraints weight = 10393.524| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4300 Z= 0.175 Angle : 0.734 11.945 5935 Z= 0.356 Chirality : 0.039 0.160 659 Planarity : 0.003 0.034 686 Dihedral : 18.743 59.699 822 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.60 % Allowed : 22.61 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.40), residues: 443 helix: 0.97 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -2.78 (0.51), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 198 HIS 0.004 0.001 HIS C 117 PHE 0.014 0.001 PHE D 175 TYR 0.017 0.002 TYR D 219 ARG 0.002 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.9495 (mp0) cc_final: 0.9213 (mp0) REVERT: C 35 MET cc_start: 0.9569 (tmm) cc_final: 0.9126 (ppp) REVERT: C 42 GLN cc_start: 0.8926 (pt0) cc_final: 0.8585 (pt0) REVERT: C 43 MET cc_start: 0.9453 (mmm) cc_final: 0.9156 (mmm) REVERT: C 62 MET cc_start: 0.8381 (mtm) cc_final: 0.7982 (mtt) REVERT: C 101 ASP cc_start: 0.9625 (t0) cc_final: 0.9408 (p0) REVERT: C 126 GLN cc_start: 0.9404 (tt0) cc_final: 0.8707 (tp40) REVERT: C 130 PHE cc_start: 0.9454 (m-10) cc_final: 0.8763 (m-80) REVERT: D 38 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9110 (mm-30) REVERT: D 110 MET cc_start: 0.8025 (tpt) cc_final: 0.7500 (tpt) REVERT: D 147 GLN cc_start: 0.8917 (mp10) cc_final: 0.8512 (mp10) REVERT: D 181 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8871 (mt-10) REVERT: D 188 PHE cc_start: 0.9438 (m-80) cc_final: 0.9144 (m-80) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 0.1843 time to fit residues: 18.4821 Evaluate side-chains 80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.066295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.046182 restraints weight = 20492.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047745 restraints weight = 13909.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048908 restraints weight = 10668.637| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4300 Z= 0.208 Angle : 0.742 10.981 5935 Z= 0.375 Chirality : 0.040 0.238 659 Planarity : 0.004 0.032 686 Dihedral : 18.847 59.968 822 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.93 % Allowed : 22.07 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.40), residues: 443 helix: 0.94 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 198 HIS 0.005 0.001 HIS C 192 PHE 0.015 0.001 PHE D 175 TYR 0.017 0.002 TYR D 219 ARG 0.002 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 GLU cc_start: 0.9451 (mp0) cc_final: 0.9222 (mp0) REVERT: C 35 MET cc_start: 0.9556 (tmm) cc_final: 0.9141 (ppp) REVERT: C 42 GLN cc_start: 0.8936 (pt0) cc_final: 0.8597 (pt0) REVERT: C 43 MET cc_start: 0.9453 (mmm) cc_final: 0.9156 (mmm) REVERT: C 62 MET cc_start: 0.8414 (mtm) cc_final: 0.7987 (mtt) REVERT: C 101 ASP cc_start: 0.9610 (t0) cc_final: 0.9409 (p0) REVERT: C 126 GLN cc_start: 0.9411 (tt0) cc_final: 0.8728 (tp40) REVERT: C 130 PHE cc_start: 0.9465 (m-10) cc_final: 0.8843 (m-80) REVERT: D 38 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9062 (mm-30) REVERT: D 110 MET cc_start: 0.7855 (tpt) cc_final: 0.7491 (tpt) REVERT: D 147 GLN cc_start: 0.8963 (mp10) cc_final: 0.8556 (mp10) REVERT: D 188 PHE cc_start: 0.9448 (m-80) cc_final: 0.9177 (m-80) REVERT: D 221 GLN cc_start: 0.9021 (mt0) cc_final: 0.8809 (mp10) outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.1808 time to fit residues: 17.3254 Evaluate side-chains 79 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.063591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043906 restraints weight = 20737.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.045324 restraints weight = 14228.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.046390 restraints weight = 11033.164| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4300 Z= 0.272 Angle : 0.803 11.691 5935 Z= 0.415 Chirality : 0.042 0.211 659 Planarity : 0.004 0.030 686 Dihedral : 19.241 59.387 822 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.66 % Allowed : 23.14 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.39), residues: 443 helix: 0.59 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.73 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 198 HIS 0.006 0.001 HIS C 192 PHE 0.018 0.002 PHE D 175 TYR 0.015 0.003 TYR D 219 ARG 0.004 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9595 (tmm) cc_final: 0.9195 (ppp) REVERT: C 43 MET cc_start: 0.9426 (mmm) cc_final: 0.9143 (tpp) REVERT: C 62 MET cc_start: 0.8504 (mtm) cc_final: 0.8130 (mtt) REVERT: C 87 ILE cc_start: 0.8908 (pt) cc_final: 0.8283 (mm) REVERT: C 126 GLN cc_start: 0.9447 (tt0) cc_final: 0.8784 (tp-100) REVERT: C 130 PHE cc_start: 0.9495 (m-10) cc_final: 0.9049 (m-80) REVERT: C 181 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8846 (mt-10) REVERT: D 35 MET cc_start: 0.9549 (ppp) cc_final: 0.9292 (ppp) REVERT: D 61 LEU cc_start: 0.9426 (mm) cc_final: 0.9202 (pp) REVERT: D 62 MET cc_start: 0.3208 (mmt) cc_final: 0.2631 (ttt) REVERT: D 110 MET cc_start: 0.7796 (tpt) cc_final: 0.7397 (tpt) REVERT: D 147 GLN cc_start: 0.9084 (mp10) cc_final: 0.8688 (mp10) REVERT: D 188 PHE cc_start: 0.9474 (m-80) cc_final: 0.9258 (m-80) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.1674 time to fit residues: 15.8038 Evaluate side-chains 74 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.0370 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.065647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.045647 restraints weight = 20229.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.047226 restraints weight = 13795.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.048356 restraints weight = 10608.997| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4300 Z= 0.211 Angle : 0.800 12.903 5935 Z= 0.402 Chirality : 0.042 0.202 659 Planarity : 0.004 0.028 686 Dihedral : 19.094 58.799 822 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.60 % Allowed : 25.27 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.39), residues: 443 helix: 0.74 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 198 HIS 0.005 0.001 HIS C 192 PHE 0.040 0.002 PHE D 175 TYR 0.017 0.002 TYR D 219 ARG 0.003 0.000 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 42 GLN cc_start: 0.9094 (pt0) cc_final: 0.8822 (pt0) REVERT: C 43 MET cc_start: 0.9460 (mmm) cc_final: 0.9183 (mmm) REVERT: C 62 MET cc_start: 0.8455 (mtm) cc_final: 0.8131 (mtt) REVERT: C 126 GLN cc_start: 0.9406 (tt0) cc_final: 0.8726 (tp40) REVERT: C 130 PHE cc_start: 0.9460 (m-10) cc_final: 0.8834 (m-80) REVERT: C 138 TYR cc_start: 0.8923 (t80) cc_final: 0.8611 (t80) REVERT: C 149 ASP cc_start: 0.9624 (m-30) cc_final: 0.9390 (p0) REVERT: C 181 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8801 (mt-10) REVERT: D 35 MET cc_start: 0.9521 (ppp) cc_final: 0.9290 (ppp) REVERT: D 61 LEU cc_start: 0.9457 (mm) cc_final: 0.9243 (pp) REVERT: D 62 MET cc_start: 0.3023 (mmt) cc_final: 0.2640 (mmt) REVERT: D 110 MET cc_start: 0.7624 (tpt) cc_final: 0.7280 (tpt) REVERT: D 147 GLN cc_start: 0.8993 (mp10) cc_final: 0.8589 (mp10) REVERT: D 188 PHE cc_start: 0.9415 (m-80) cc_final: 0.9107 (m-80) REVERT: D 221 GLN cc_start: 0.9018 (mt0) cc_final: 0.8812 (mp10) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.1682 time to fit residues: 16.7639 Evaluate side-chains 78 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 32 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.064743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045023 restraints weight = 20373.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.046559 restraints weight = 13805.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.047691 restraints weight = 10605.522| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4300 Z= 0.235 Angle : 0.856 12.914 5935 Z= 0.431 Chirality : 0.043 0.232 659 Planarity : 0.004 0.029 686 Dihedral : 19.033 58.776 822 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.13 % Allowed : 26.06 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.39), residues: 443 helix: 0.68 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -2.64 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 198 HIS 0.005 0.001 HIS C 192 PHE 0.040 0.002 PHE D 175 TYR 0.016 0.002 TYR D 219 ARG 0.004 0.000 ARG D 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9622 (tmm) cc_final: 0.9243 (ppp) REVERT: C 42 GLN cc_start: 0.9111 (pt0) cc_final: 0.8829 (pt0) REVERT: C 43 MET cc_start: 0.9484 (mmm) cc_final: 0.9210 (mmm) REVERT: C 62 MET cc_start: 0.8539 (mtm) cc_final: 0.8184 (mtt) REVERT: C 87 ILE cc_start: 0.8981 (pt) cc_final: 0.8377 (mm) REVERT: C 126 GLN cc_start: 0.9394 (tt0) cc_final: 0.8742 (tp-100) REVERT: C 130 PHE cc_start: 0.9463 (m-10) cc_final: 0.8947 (m-80) REVERT: C 138 TYR cc_start: 0.8935 (t80) cc_final: 0.8631 (t80) REVERT: C 149 ASP cc_start: 0.9639 (m-30) cc_final: 0.9396 (p0) REVERT: D 35 MET cc_start: 0.9503 (ppp) cc_final: 0.9288 (ppp) REVERT: D 62 MET cc_start: 0.3063 (mmt) cc_final: 0.2515 (ttt) REVERT: D 110 MET cc_start: 0.7775 (tpt) cc_final: 0.7438 (tpt) REVERT: D 112 LYS cc_start: 0.9360 (mttt) cc_final: 0.8746 (mmtt) REVERT: D 147 GLN cc_start: 0.9017 (mp10) cc_final: 0.8599 (mp10) REVERT: D 153 LYS cc_start: 0.9553 (pttm) cc_final: 0.9144 (tppt) REVERT: D 156 GLU cc_start: 0.9741 (mt-10) cc_final: 0.9486 (mp0) REVERT: D 188 PHE cc_start: 0.9432 (m-80) cc_final: 0.9161 (m-80) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.1699 time to fit residues: 17.1884 Evaluate side-chains 77 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 HIS C 242 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.066837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.047984 restraints weight = 20730.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.049619 restraints weight = 13638.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.050832 restraints weight = 10234.262| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4300 Z= 0.218 Angle : 0.871 12.833 5935 Z= 0.437 Chirality : 0.043 0.212 659 Planarity : 0.004 0.029 686 Dihedral : 19.031 58.586 822 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.39 % Allowed : 26.06 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.40), residues: 443 helix: 0.71 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -2.60 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 198 HIS 0.004 0.001 HIS C 192 PHE 0.038 0.002 PHE D 175 TYR 0.026 0.003 TYR D 219 ARG 0.004 0.000 ARG D 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.55 seconds wall clock time: 30 minutes 22.73 seconds (1822.73 seconds total)