Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:22:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/04_2023/6wfq_21652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/04_2023/6wfq_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_21652/04_2023/6wfq_21652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/04_2023/6wfq_21652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/04_2023/6wfq_21652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wfq_21652/04_2023/6wfq_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 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 2.98, 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: 2.05 Conformation dependent library (CDL) restraints added in 673.0 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: 1.18 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: 1.05 Time building geometry restraints manager: 2.21 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 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: 0.530 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: 2.490 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.590 Find NCS groups from input model: 0.200 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- 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 : 16.661 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 : 0.456 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: 0.1727 time to fit residues: 25.7867 Evaluate side-chains 69 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6089 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2573 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= 0.198 Angle : 0.677 12.480 5935 Z= 0.339 Chirality : 0.038 0.200 659 Planarity : 0.004 0.028 686 Dihedral : 18.091 59.329 782 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -0.79 (0.39), residues: 443 helix: 0.55 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -3.52 (0.47), 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: 5 poor density : 73 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.1781 time to fit residues: 16.4905 Evaluate side-chains 71 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0417 time to fit residues: 0.7913 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8071 moved from start: 0.3068 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= 0.178 Angle : 0.670 10.191 5935 Z= 0.337 Chirality : 0.037 0.126 659 Planarity : 0.003 0.034 686 Dihedral : 18.140 58.979 782 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.60 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: -0.47 (0.40), residues: 443 helix: 0.74 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -3.32 (0.48), 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 78 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.1665 time to fit residues: 15.8764 Evaluate side-chains 71 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.445 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0503 time to fit residues: 0.8468 ------------------------------------------------------------------------------- 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: 4.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN C 164 ASN C 215 ASN D 126 GLN D 192 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 4300 Z= 0.206 Angle : 0.679 10.021 5935 Z= 0.350 Chirality : 0.038 0.146 659 Planarity : 0.004 0.032 686 Dihedral : 18.309 59.216 782 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: -0.27 (0.40), residues: 443 helix: 0.81 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.03 (0.49), residues: 118 *********************** 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: 7 poor density : 72 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: 2 residues processed: 77 average time/residue: 0.1708 time to fit residues: 16.4491 Evaluate side-chains 64 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.474 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0561 time to fit residues: 0.8004 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8085 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 4300 Z= 0.181 Angle : 0.700 12.106 5935 Z= 0.350 Chirality : 0.039 0.196 659 Planarity : 0.003 0.026 686 Dihedral : 18.403 58.743 782 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: -0.15 (0.40), residues: 443 helix: 0.85 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.80 (0.50), residues: 118 *********************** 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 79 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.1639 time to fit residues: 16.0087 Evaluate side-chains 66 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.468 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0527 time to fit residues: 0.8767 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.0000 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 4300 Z= 0.214 Angle : 0.755 13.895 5935 Z= 0.379 Chirality : 0.040 0.174 659 Planarity : 0.004 0.033 686 Dihedral : 18.682 58.773 782 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % 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: -0.18 (0.40), residues: 443 helix: 0.75 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.54 (0.53), residues: 118 *********************** 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 69 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 0.1756 time to fit residues: 14.9761 Evaluate side-chains 66 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1629 time to fit residues: 1.3959 ------------------------------------------------------------------------------- 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: 5.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 0.0060 chunk 29 optimal weight: 8.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 4300 Z= 0.209 Angle : 0.755 14.531 5935 Z= 0.380 Chirality : 0.040 0.157 659 Planarity : 0.004 0.026 686 Dihedral : 19.044 58.821 782 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.27 % 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: -0.28 (0.39), residues: 443 helix: 0.66 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.55 (0.52), residues: 117 *********************** 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 71 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1785 time to fit residues: 15.5321 Evaluate side-chains 68 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0620 time to fit residues: 0.6864 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.0370 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 126 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4493 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= 0.190 Angle : 0.781 13.884 5935 Z= 0.382 Chirality : 0.042 0.313 659 Planarity : 0.004 0.027 686 Dihedral : 18.956 59.021 782 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: 0.80 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.34 (0.53), residues: 118 *********************** 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 73 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 0.1734 time to fit residues: 15.5818 Evaluate side-chains 70 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0676 time to fit residues: 0.6997 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 0.0270 overall best weight: 1.7444 ------------------------------------------------------------------------------- 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 126 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4300 Z= 0.197 Angle : 0.823 17.824 5935 Z= 0.397 Chirality : 0.044 0.339 659 Planarity : 0.004 0.028 686 Dihedral : 18.998 58.984 782 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: -0.17 (0.40), residues: 443 helix: 0.68 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.30 (0.53), residues: 117 *********************** 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 74 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 73 average time/residue: 0.1767 time to fit residues: 16.3656 Evaluate side-chains 66 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6094 ------------------------------------------------------------------------------- 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: 7.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 242 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 4300 Z= 0.233 Angle : 0.854 11.982 5935 Z= 0.426 Chirality : 0.044 0.293 659 Planarity : 0.004 0.029 686 Dihedral : 19.129 59.539 782 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -0.37 (0.39), residues: 443 helix: 0.55 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -2.45 (0.52), residues: 117 ********************** 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: 7 poor density : 66 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1884 time to fit residues: 16.1284 Evaluate side-chains 70 residues out of total 376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0564 time to fit residues: 0.9743 ------------------------------------------------------------------------------- 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: 6.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 25 optimal weight: 40.0000 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.065571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.045159 restraints weight = 21036.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.046754 restraints weight = 14163.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047933 restraints weight = 10853.921| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4908 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= 0.203 Angle : 0.880 19.417 5935 Z= 0.420 Chirality : 0.044 0.339 659 Planarity : 0.004 0.029 686 Dihedral : 19.109 59.844 782 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.00 % 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: -0.17 (0.39), residues: 443 helix: 0.68 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -2.21 (0.52), residues: 121 =============================================================================== Job complete usr+sys time: 1036.15 seconds wall clock time: 19 minutes 20.63 seconds (1160.63 seconds total)