Starting phenix.real_space_refine on Sun Mar 10 18:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/03_2024/6wfq_21652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/03_2024/6wfq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/03_2024/6wfq_21652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/03_2024/6wfq_21652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/03_2024/6wfq_21652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/03_2024/6wfq_21652.pdb" } 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 Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.99, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 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: 1.79 Conformation dependent library (CDL) restraints added in 628.2 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: 1.45 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: 1.89 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: 100.80 - 107.43: 316 107.43 - 114.06: 2425 114.06 - 120.69: 1897 120.69 - 127.32: 1212 127.32 - 133.96: 85 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 2.440 nonbonded pdb=" O LEU D 211 " pdb=" ND2 ASN D 215 " model vdw 2.360 2.520 nonbonded pdb=" O SER C 99 " pdb=" OG1 THR C 102 " model vdw 2.390 2.440 nonbonded pdb=" O ASN D 158 " pdb=" OG SER D 161 " model vdw 2.399 2.440 nonbonded pdb=" O GLU C 156 " pdb=" OG SER C 159 " model vdw 2.399 2.440 ... (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 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: 0.490 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: 2.450 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.010 Find NCS groups from input model: 0.210 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.462 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: 0.1703 time to fit residues: 25.4753 Evaluate side-chains 74 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 214 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4300 Z= 0.245 Angle : 0.683 10.406 5935 Z= 0.354 Chirality : 0.039 0.189 659 Planarity : 0.004 0.029 686 Dihedral : 18.437 58.892 822 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.60 % Allowed : 17.02 % Favored : 81.38 % 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: -0.89 (0.39), residues: 443 helix: 0.45 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.52 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 198 HIS 0.005 0.001 HIS D 192 PHE 0.010 0.001 PHE D 65 TYR 0.021 0.003 TYR C 219 ARG 0.004 0.001 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 80 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.395 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: 0.9544 (tmm) cc_final: 0.9198 (ppp) REVERT: C 126 GLN cc_start: 0.9439 (tt0) cc_final: 0.8642 (tp-100) REVERT: C 130 PHE cc_start: 0.9451 (m-10) cc_final: 0.8845 (m-80) REVERT: C 153 LYS cc_start: 0.9772 (pptt) cc_final: 0.9504 (tptt) REVERT: C 157 ILE cc_start: 0.9492 (tp) cc_final: 0.9158 (tp) REVERT: C 181 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8910 (mt-10) REVERT: C 212 HIS cc_start: 0.9479 (p-80) cc_final: 0.9230 (m-70) REVERT: D 35 MET cc_start: 0.9586 (tmm) cc_final: 0.9342 (ppp) REVERT: D 97 ARG cc_start: 0.8975 (mmp80) cc_final: 0.8254 (mmp80) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.1667 time to fit residues: 16.0688 Evaluate side-chains 73 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4300 Z= 0.225 Angle : 0.659 9.829 5935 Z= 0.344 Chirality : 0.038 0.134 659 Planarity : 0.004 0.031 686 Dihedral : 18.549 59.642 822 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.93 % Allowed : 19.15 % Favored : 77.93 % 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: -0.72 (0.39), residues: 443 helix: 0.53 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.29 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 198 HIS 0.004 0.001 HIS D 222 PHE 0.016 0.001 PHE D 114 TYR 0.038 0.004 TYR C 219 ARG 0.003 0.000 ARG D 69 *********************** 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 85 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.9506 (pp20) cc_final: 0.9299 (pp20) REVERT: C 62 MET cc_start: 0.9159 (tmm) cc_final: 0.8925 (ptp) REVERT: C 126 GLN cc_start: 0.9436 (tt0) cc_final: 0.8690 (tp40) REVERT: C 130 PHE cc_start: 0.9485 (m-10) cc_final: 0.8878 (m-80) REVERT: C 138 TYR cc_start: 0.9042 (t80) cc_final: 0.8679 (t80) REVERT: C 181 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8830 (mt-10) REVERT: C 212 HIS cc_start: 0.9496 (p-80) cc_final: 0.9182 (m-70) REVERT: D 42 GLN cc_start: 0.9509 (tp40) cc_final: 0.9240 (tm-30) REVERT: D 43 MET cc_start: 0.9409 (mmt) cc_final: 0.8899 (mmt) REVERT: D 62 MET cc_start: 0.1758 (ttt) cc_final: 0.1317 (tpp) REVERT: D 97 ARG cc_start: 0.9094 (mmp80) cc_final: 0.8375 (mmp80) REVERT: D 181 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8906 (mt-10) REVERT: D 188 PHE cc_start: 0.9477 (m-80) cc_final: 0.9217 (m-80) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.1662 time to fit residues: 16.4324 Evaluate side-chains 76 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 C residue 235 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4300 Z= 0.193 Angle : 0.681 11.387 5935 Z= 0.346 Chirality : 0.039 0.162 659 Planarity : 0.003 0.027 686 Dihedral : 18.661 59.949 822 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.39 % Allowed : 20.74 % Favored : 76.86 % 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: -0.38 (0.39), residues: 443 helix: 0.74 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -3.14 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 198 HIS 0.006 0.001 HIS D 192 PHE 0.008 0.001 PHE D 188 TYR 0.035 0.004 TYR C 219 ARG 0.002 0.000 ARG C 94 *********************** 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 85 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9590 (tmm) cc_final: 0.9220 (ppp) REVERT: C 37 GLU cc_start: 0.9547 (pp20) cc_final: 0.9324 (pp20) REVERT: C 126 GLN cc_start: 0.9409 (tt0) cc_final: 0.8643 (tp40) REVERT: C 130 PHE cc_start: 0.9465 (m-10) cc_final: 0.8799 (m-80) REVERT: C 138 TYR cc_start: 0.8995 (t80) cc_final: 0.8602 (t80) REVERT: C 181 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8856 (mt-10) REVERT: C 212 HIS cc_start: 0.9466 (p-80) cc_final: 0.9134 (m-70) REVERT: D 110 MET cc_start: 0.8178 (tpt) cc_final: 0.7750 (tpt) REVERT: D 181 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8853 (mt-10) REVERT: D 188 PHE cc_start: 0.9472 (m-80) cc_final: 0.9228 (m-80) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.1608 time to fit residues: 16.5439 Evaluate side-chains 83 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 C residue 235 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 0.0470 chunk 25 optimal weight: 30.0000 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4300 Z= 0.187 Angle : 0.704 10.875 5935 Z= 0.351 Chirality : 0.039 0.177 659 Planarity : 0.004 0.033 686 Dihedral : 18.829 59.290 822 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.13 % Allowed : 22.61 % Favored : 75.27 % 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: -0.18 (0.40), residues: 443 helix: 0.84 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.91 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 198 HIS 0.004 0.001 HIS C 117 PHE 0.017 0.001 PHE D 114 TYR 0.034 0.004 TYR C 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 84 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.320 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: 0.9609 (tmm) cc_final: 0.9244 (ppp) REVERT: C 37 GLU cc_start: 0.9571 (pp20) cc_final: 0.9319 (pp20) REVERT: C 126 GLN cc_start: 0.9398 (tt0) cc_final: 0.8634 (tp40) REVERT: C 130 PHE cc_start: 0.9487 (m-10) cc_final: 0.8807 (m-80) REVERT: C 138 TYR cc_start: 0.8966 (t80) cc_final: 0.8550 (t80) REVERT: C 181 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8867 (mt-10) REVERT: D 110 MET cc_start: 0.8043 (tpt) cc_final: 0.7702 (tpt) REVERT: D 147 GLN cc_start: 0.9014 (mp10) cc_final: 0.8648 (mp10) REVERT: D 188 PHE cc_start: 0.9461 (m-80) cc_final: 0.9177 (m-80) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.1304 time to fit residues: 13.1338 Evaluate side-chains 80 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 C residue 235 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4300 Z= 0.201 Angle : 0.704 10.650 5935 Z= 0.357 Chirality : 0.039 0.155 659 Planarity : 0.004 0.030 686 Dihedral : 19.097 59.761 822 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -0.14 (0.40), residues: 443 helix: 0.84 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.77 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 198 HIS 0.004 0.001 HIS C 117 PHE 0.016 0.001 PHE D 114 TYR 0.034 0.004 TYR C 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 fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9625 (tmm) cc_final: 0.9271 (ppp) REVERT: C 37 GLU cc_start: 0.9593 (pp20) cc_final: 0.9330 (pp20) REVERT: C 126 GLN cc_start: 0.9393 (tt0) cc_final: 0.8667 (tp40) REVERT: C 130 PHE cc_start: 0.9483 (m-10) cc_final: 0.8837 (m-80) REVERT: C 181 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8888 (mt-10) REVERT: D 62 MET cc_start: 0.1166 (ttt) cc_final: 0.0936 (mmt) REVERT: D 110 MET cc_start: 0.8105 (tpt) cc_final: 0.7641 (tpp) REVERT: D 147 GLN cc_start: 0.8998 (mp10) cc_final: 0.8646 (mp10) REVERT: D 157 ILE cc_start: 0.9787 (OUTLIER) cc_final: 0.9569 (tp) REVERT: D 188 PHE cc_start: 0.9472 (m-80) cc_final: 0.9225 (m-80) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.1575 time to fit residues: 16.2300 Evaluate side-chains 83 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 C residue 235 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 242 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4300 Z= 0.185 Angle : 0.716 11.568 5935 Z= 0.360 Chirality : 0.039 0.213 659 Planarity : 0.003 0.032 686 Dihedral : 19.110 59.852 822 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.99 % Allowed : 22.87 % 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: -0.02 (0.40), residues: 443 helix: 0.92 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.70 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP D 198 HIS 0.004 0.001 HIS C 117 PHE 0.014 0.001 PHE D 114 TYR 0.033 0.004 TYR C 219 ARG 0.002 0.000 ARG D 45 *********************** 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 89 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9629 (tmm) cc_final: 0.9270 (ppp) REVERT: C 37 GLU cc_start: 0.9593 (pp20) cc_final: 0.9323 (pp20) REVERT: C 126 GLN cc_start: 0.9388 (tt0) cc_final: 0.8651 (tp40) REVERT: C 130 PHE cc_start: 0.9488 (m-10) cc_final: 0.8819 (m-80) REVERT: C 138 TYR cc_start: 0.8954 (t80) cc_final: 0.8646 (t80) REVERT: C 181 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8854 (mt-10) REVERT: D 110 MET cc_start: 0.8045 (tpt) cc_final: 0.7592 (tpp) REVERT: D 147 GLN cc_start: 0.8976 (mp10) cc_final: 0.8619 (mp10) REVERT: D 157 ILE cc_start: 0.9794 (OUTLIER) cc_final: 0.9585 (tp) REVERT: D 188 PHE cc_start: 0.9472 (m-80) cc_final: 0.9214 (m-80) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.1495 time to fit residues: 15.7300 Evaluate side-chains 85 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 149 ASP 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 C residue 235 ASP Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.0070 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4439 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 : 0.776 17.278 5935 Z= 0.377 Chirality : 0.039 0.191 659 Planarity : 0.003 0.031 686 Dihedral : 19.135 59.783 822 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.46 % Allowed : 23.40 % 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: 0.04 (0.40), residues: 443 helix: 0.93 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.54 (0.51), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 198 HIS 0.005 0.001 HIS D 192 PHE 0.014 0.001 PHE D 114 TYR 0.032 0.003 TYR C 219 ARG 0.003 0.000 ARG C 94 *********************** 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 91 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.400 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: 0.9627 (tmm) cc_final: 0.9268 (ppp) REVERT: C 37 GLU cc_start: 0.9579 (pp20) cc_final: 0.9312 (pp20) REVERT: C 126 GLN cc_start: 0.9381 (tt0) cc_final: 0.8633 (tp40) REVERT: C 130 PHE cc_start: 0.9459 (m-10) cc_final: 0.8743 (m-80) REVERT: C 138 TYR cc_start: 0.8935 (t80) cc_final: 0.8617 (t80) REVERT: C 181 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8835 (mt-10) REVERT: D 62 MET cc_start: 0.1257 (ttt) cc_final: 0.0844 (tpp) REVERT: D 110 MET cc_start: 0.8033 (tpt) cc_final: 0.7541 (tpp) REVERT: D 147 GLN cc_start: 0.8947 (mp10) cc_final: 0.8590 (mp10) REVERT: D 188 PHE cc_start: 0.9451 (m-80) cc_final: 0.9177 (m-80) outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.1441 time to fit residues: 15.6535 Evaluate side-chains 83 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 HIS 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 C residue 235 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4300 Z= 0.202 Angle : 0.780 16.747 5935 Z= 0.385 Chirality : 0.040 0.178 659 Planarity : 0.003 0.031 686 Dihedral : 19.168 59.569 822 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.46 % Allowed : 23.40 % 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: -0.06 (0.40), residues: 443 helix: 0.83 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.50 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 198 HIS 0.006 0.001 HIS D 192 PHE 0.015 0.001 PHE D 114 TYR 0.033 0.004 TYR C 219 ARG 0.002 0.000 ARG C 94 *********************** 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 85 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.462 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: 0.9633 (tmm) cc_final: 0.9278 (ppp) REVERT: C 37 GLU cc_start: 0.9599 (pp20) cc_final: 0.9334 (pp20) REVERT: C 126 GLN cc_start: 0.9380 (tt0) cc_final: 0.8675 (tp40) REVERT: C 130 PHE cc_start: 0.9428 (m-10) cc_final: 0.8827 (m-80) REVERT: C 138 TYR cc_start: 0.8952 (t80) cc_final: 0.8620 (t80) REVERT: C 181 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8855 (mt-10) REVERT: D 62 MET cc_start: 0.1334 (ttt) cc_final: 0.0938 (tpp) REVERT: D 110 MET cc_start: 0.8092 (tpt) cc_final: 0.7676 (tpp) REVERT: D 112 LYS cc_start: 0.9218 (mmmm) cc_final: 0.9003 (mmmt) REVERT: D 147 GLN cc_start: 0.8970 (mp10) cc_final: 0.8616 (mp10) REVERT: D 188 PHE cc_start: 0.9447 (m-80) cc_final: 0.9173 (m-80) outliers start: 13 outliers final: 13 residues processed: 81 average time/residue: 0.1558 time to fit residues: 15.9876 Evaluate side-chains 82 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 142 HIS 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 C residue 235 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.0020 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4518 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= 0.183 Angle : 0.840 17.984 5935 Z= 0.397 Chirality : 0.041 0.181 659 Planarity : 0.003 0.031 686 Dihedral : 19.182 59.814 822 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.66 % Allowed : 24.20 % 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: -0.03 (0.40), residues: 443 helix: 0.86 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.54 (0.51), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 198 HIS 0.005 0.001 HIS D 192 PHE 0.011 0.001 PHE D 114 TYR 0.031 0.003 TYR C 219 ARG 0.002 0.000 ARG C 128 ********************** 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 85 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 MET cc_start: 0.9616 (tmm) cc_final: 0.9256 (ppp) REVERT: C 37 GLU cc_start: 0.9552 (pp20) cc_final: 0.9280 (pp20) REVERT: C 126 GLN cc_start: 0.9355 (tt0) cc_final: 0.8630 (tp-100) REVERT: C 130 PHE cc_start: 0.9444 (m-10) cc_final: 0.8710 (m-80) REVERT: C 138 TYR cc_start: 0.8860 (t80) cc_final: 0.8549 (t80) REVERT: D 35 MET cc_start: 0.9568 (ppp) cc_final: 0.9283 (ppp) REVERT: D 38 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9031 (mm-30) REVERT: D 62 MET cc_start: 0.1380 (ttt) cc_final: 0.1054 (mmt) REVERT: D 112 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8941 (mmmt) REVERT: D 147 GLN cc_start: 0.8843 (mp10) cc_final: 0.8476 (mp10) REVERT: D 188 PHE cc_start: 0.9421 (m-80) cc_final: 0.9099 (m-80) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.1543 time to fit residues: 15.7918 Evaluate side-chains 82 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 221 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** 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 = 0.3670 r_free = 0.3670 target = 0.062953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043809 restraints weight = 21124.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.045333 restraints weight = 14189.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046400 restraints weight = 10888.416| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4300 Z= 0.253 Angle : 0.841 15.515 5935 Z= 0.421 Chirality : 0.041 0.177 659 Planarity : 0.004 0.033 686 Dihedral : 19.254 59.773 822 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.66 % Allowed : 25.53 % 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: -0.30 (0.39), residues: 443 helix: 0.59 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.37 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 198 HIS 0.009 0.001 HIS D 192 PHE 0.018 0.002 PHE D 114 TYR 0.041 0.005 TYR C 219 ARG 0.003 0.000 ARG C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.24 seconds wall clock time: 21 minutes 15.72 seconds (1275.72 seconds total)