Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:15:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/11_2022/6wfq_21652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/11_2022/6wfq_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_21652/11_2022/6wfq_21652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/11_2022/6wfq_21652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/11_2022/6wfq_21652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/11_2022/6wfq_21652.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.94, per 1000 atoms: 0.71 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: 2.22 Conformation dependent library (CDL) restraints added in 554.8 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: 1.07 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: 0.93 Time building geometry restraints manager: 2.17 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: 2166 16.59 - 33.17: 207 33.17 - 49.76: 102 49.76 - 66.34: 37 66.34 - 82.93: 2 Dihedral angle restraints: 2514 sinusoidal: 1211 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 2511 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 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. 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: 0.420 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: 2.600 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 16.560 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 16.661 82.929 1660 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 % 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 *********************** 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 : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 122 average time/residue: 0.1675 time to fit residues: 25.2062 Evaluate side-chains 69 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5990 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** ** C 164 ASN ** 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: 0.7981 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4300 Z= 0.240 Angle : 0.696 12.303 5935 Z= 0.354 Chirality : 0.039 0.200 659 Planarity : 0.004 0.028 686 Dihedral : 18.132 59.625 782 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.60 % 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: -0.82 (0.39), residues: 443 helix: 0.52 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -3.50 (0.48), residues: 121 *********************** 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 78 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.1625 time to fit residues: 15.3591 Evaluate side-chains 67 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0436 time to fit residues: 0.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN D 192 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3170 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= 0.183 Angle : 0.668 10.092 5935 Z= 0.338 Chirality : 0.038 0.153 659 Planarity : 0.004 0.032 686 Dihedral : 18.192 59.511 782 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.06 % 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: -0.62 (0.39), residues: 443 helix: 0.61 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -3.31 (0.47), residues: 119 *********************** 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 80 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 80 average time/residue: 0.1627 time to fit residues: 16.3899 Evaluate side-chains 66 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.473 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0676 time to fit residues: 0.7112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN C 126 GLN C 215 ASN C 242 GLN D 126 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3465 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= 0.167 Angle : 0.679 10.573 5935 Z= 0.340 Chirality : 0.039 0.180 659 Planarity : 0.003 0.031 686 Dihedral : 18.281 59.528 782 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 1.33 % 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: -0.37 (0.40), residues: 443 helix: 0.77 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -3.14 (0.47), residues: 119 *********************** 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 79 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.1527 time to fit residues: 14.4370 Evaluate side-chains 71 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.456 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0553 time to fit residues: 0.7741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 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 126 GLN 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: 0.8028 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4300 Z= 0.241 Angle : 0.724 10.534 5935 Z= 0.371 Chirality : 0.041 0.226 659 Planarity : 0.004 0.031 686 Dihedral : 18.663 59.613 782 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 1.86 % 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: -0.39 (0.40), residues: 443 helix: 0.66 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -2.91 (0.53), residues: 116 *********************** 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 76 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 0.1624 time to fit residues: 14.7764 Evaluate side-chains 70 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.454 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0510 time to fit residues: 1.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 0.0170 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 overall best weight: 1.0422 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4122 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= 0.180 Angle : 0.721 12.889 5935 Z= 0.355 Chirality : 0.039 0.199 659 Planarity : 0.003 0.030 686 Dihedral : 18.790 59.366 782 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 1.33 % 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: 326 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 117 *********************** 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 74 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1730 time to fit residues: 15.3084 Evaluate side-chains 72 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.451 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1367 time to fit residues: 1.4616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN C 126 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: 0.7955 moved from start: 0.4267 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= 0.177 Angle : 0.740 11.642 5935 Z= 0.370 Chirality : 0.040 0.166 659 Planarity : 0.003 0.027 686 Dihedral : 18.861 58.924 782 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.80 % 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: 0.04 (0.40), residues: 443 helix: 0.94 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.58 (0.52), residues: 118 *********************** 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 76 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.1687 time to fit residues: 15.8653 Evaluate side-chains 68 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0689 time to fit residues: 0.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4425 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= 0.188 Angle : 0.805 17.412 5935 Z= 0.392 Chirality : 0.042 0.243 659 Planarity : 0.004 0.027 686 Dihedral : 18.880 58.859 782 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 1.33 % 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: 0.85 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -2.41 (0.53), residues: 119 *********************** 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 76 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.1730 time to fit residues: 16.4048 Evaluate side-chains 70 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0457 time to fit residues: 0.9024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 0.0270 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4541 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= 0.193 Angle : 0.843 17.606 5935 Z= 0.413 Chirality : 0.043 0.225 659 Planarity : 0.004 0.027 686 Dihedral : 18.904 58.964 782 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 1.33 % 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: 0.81 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.31 (0.53), residues: 120 *********************** 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 75 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1850 time to fit residues: 16.1755 Evaluate side-chains 71 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0616 time to fit residues: 1.0506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4645 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= 0.197 Angle : 0.849 17.217 5935 Z= 0.418 Chirality : 0.043 0.215 659 Planarity : 0.005 0.073 686 Dihedral : 18.888 58.831 782 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.53 % 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: -0.08 (0.40), residues: 443 helix: 0.78 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.26 (0.52), residues: 122 ********************** 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 73 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.1695 time to fit residues: 15.2660 Evaluate side-chains 69 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0571 time to fit residues: 0.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 40.0000 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 0.0000 chunk 27 optimal weight: 20.0000 overall best weight: 2.2390 ------------------------------------------------------------------------------- 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** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.065284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045372 restraints weight = 20628.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.046905 restraints weight = 14136.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.048007 restraints weight = 10891.580| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 4300 Z= 0.219 Angle : 0.828 12.393 5935 Z= 0.418 Chirality : 0.043 0.204 659 Planarity : 0.005 0.068 686 Dihedral : 19.017 59.104 782 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.80 % 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: -0.24 (0.39), residues: 443 helix: 0.62 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.24 (0.53), residues: 121 =============================================================================== Job complete usr+sys time: 1071.06 seconds wall clock time: 20 minutes 36.98 seconds (1236.98 seconds total)