Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 04:41:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/04_2023/8dmb_27533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/04_2023/8dmb_27533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/04_2023/8dmb_27533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/04_2023/8dmb_27533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/04_2023/8dmb_27533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/04_2023/8dmb_27533.pdb" } resolution = 3.1 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= 0.006 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: 7 Type Number sf(0) Gaussians P 274 5.49 5 Mg 2 5.21 5 S 9 5.16 5 C 4303 2.51 5 N 1586 2.21 5 O 2323 1.98 5 H 5728 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 14225 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 5376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5376 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 7634 Classifications: {'RNA': 237} Modifications used: {'3*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 109, 'rna3p_pyr': 103} Link IDs: {'rna2p': 25, 'rna3p': 211} Chain breaks: 4 Chain: "X" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 893 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "Y" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.42, per 1000 atoms: 0.52 Number of scatterers: 14225 At special positions: 0 Unit cell: (108.68, 128.128, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 9 16.00 P 274 15.00 Mg 2 11.99 O 2323 8.00 N 1586 7.00 C 4303 6.00 H 5728 1.00 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: 13.71 Conformation dependent library (CDL) restraints added in 732.9 milliseconds 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 3 sheets defined 34.5% alpha, 21.3% beta 108 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'P' and resid 22 through 32 Processing helix chain 'P' and resid 92 through 112 Processing helix chain 'P' and resid 130 through 151 removed outlier: 4.105A pdb=" N ILE P 150 " --> pdb=" O GLU P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 168 Processing helix chain 'P' and resid 171 through 179 removed outlier: 4.974A pdb=" N VAL P 177 " --> pdb=" O TYR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 192 removed outlier: 3.668A pdb=" N LYS P 190 " --> pdb=" O ARG P 186 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 210 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 267 through 271 removed outlier: 3.581A pdb=" N VAL P 271 " --> pdb=" O LYS P 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.201A pdb=" N VAL P 11 " --> pdb=" O MET P 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 193 through 197 removed outlier: 3.640A pdb=" N LEU P 155 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU P 159 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER P 77 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N PHE P 249 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG P 84 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TRP P 251 " --> pdb=" O ARG P 84 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET P 86 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG P 253 " --> pdb=" O MET P 86 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE P 88 " --> pdb=" O ARG P 253 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE P 248 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG P 252 " --> pdb=" O SER P 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 323 through 327 removed outlier: 6.074A pdb=" N GLY P 315 " --> pdb=" O CYS P 304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU P 291 " --> pdb=" O LEU P 334 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU P 334 " --> pdb=" O GLU P 291 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 293 " --> pdb=" O VAL P 332 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL P 332 " --> pdb=" O GLU P 293 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 526 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 13.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 5725 1.02 - 1.22: 5 1.22 - 1.41: 3882 1.41 - 1.61: 5326 1.61 - 1.81: 29 Bond restraints: 14967 Sorted by residual: bond pdb=" C ALA P 130 " pdb=" N PRO P 131 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.51e-02 4.39e+03 6.50e+00 bond pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " ideal model delta sigma weight residual 1.422 1.498 -0.076 3.00e-02 1.11e+03 6.34e+00 bond pdb=" C TYR P 151 " pdb=" N PRO P 152 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.47e+00 bond pdb=" C1' DT Y 2 " pdb=" N1 DT Y 2 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" C4' U W 19 " pdb=" C3' U W 19 " ideal model delta sigma weight residual 1.521 1.491 0.030 1.50e-02 4.44e+03 3.97e+00 ... (remaining 14962 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 1658 106.25 - 113.19: 14917 113.19 - 120.12: 5670 120.12 - 127.05: 3988 127.05 - 133.99: 639 Bond angle restraints: 26872 Sorted by residual: angle pdb=" O3' DT Y 2 " pdb=" C3' DT Y 2 " pdb=" C2' DT Y 2 " ideal model delta sigma weight residual 111.50 119.49 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " pdb=" P DG Y 3 " ideal model delta sigma weight residual 120.20 127.04 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" C2' A W 11 " pdb=" C1' A W 11 " pdb=" N9 A W 11 " ideal model delta sigma weight residual 112.00 118.06 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C2' A W 251 " pdb=" C1' A W 251 " pdb=" N9 A W 251 " ideal model delta sigma weight residual 112.00 117.64 -5.64 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C5' U W 19 " pdb=" C4' U W 19 " pdb=" O4' U W 19 " ideal model delta sigma weight residual 109.80 115.42 -5.62 1.50e+00 4.44e-01 1.40e+01 ... (remaining 26867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 5486 35.62 - 71.23: 298 71.23 - 106.84: 66 106.84 - 142.46: 1 142.46 - 178.07: 2 Dihedral angle restraints: 5853 sinusoidal: 4750 harmonic: 1103 Sorted by residual: dihedral pdb=" O4' U W 255 " pdb=" C1' U W 255 " pdb=" N1 U W 255 " pdb=" C2 U W 255 " ideal model delta sinusoidal sigma weight residual 232.00 53.93 178.07 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C W 146 " pdb=" C1' C W 146 " pdb=" N1 C W 146 " pdb=" C2 C W 146 " ideal model delta sinusoidal sigma weight residual -128.00 44.32 -172.32 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C W 147 " pdb=" C1' C W 147 " pdb=" N1 C W 147 " pdb=" C2 C W 147 " ideal model delta sinusoidal sigma weight residual -160.00 -86.23 -73.77 1 1.50e+01 4.44e-03 3.07e+01 ... (remaining 5850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1316 0.052 - 0.104: 319 0.104 - 0.157: 70 0.157 - 0.209: 10 0.209 - 0.261: 7 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C1' A W 11 " pdb=" O4' A W 11 " pdb=" C2' A W 11 " pdb=" N9 A W 11 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1' A W 251 " pdb=" O4' A W 251 " pdb=" C2' A W 251 " pdb=" N9 A W 251 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1' A W 189 " pdb=" O4' A W 189 " pdb=" C2' A W 189 " pdb=" N9 A W 189 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1719 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 108 " 0.369 9.50e-02 1.11e+02 1.25e-01 2.38e+01 pdb=" NE ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG P 108 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG P 108 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 108 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG P 108 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG P 108 " 0.024 2.00e-02 2.50e+03 pdb="HH21 ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 108 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 253 " 0.295 9.50e-02 1.11e+02 1.00e-01 1.75e+01 pdb=" NE ARG P 253 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG P 253 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG P 253 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 253 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG P 253 " 0.025 2.00e-02 2.50e+03 pdb="HH21 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 253 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN P 170 " 0.025 2.00e-02 2.50e+03 3.26e-02 1.59e+01 pdb=" CG ASN P 170 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN P 170 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN P 170 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN P 170 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN P 170 " 0.049 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1437 2.26 - 2.85: 24223 2.85 - 3.43: 33487 3.43 - 4.02: 52883 4.02 - 4.60: 74867 Nonbonded interactions: 186897 Sorted by model distance: nonbonded pdb="HO2' A W 152 " pdb=" OP2 U W 154 " model vdw 1.677 1.850 nonbonded pdb="HO2' G W 72 " pdb=" O2 C W 98 " model vdw 1.688 1.850 nonbonded pdb=" HZ1 LYS P 142 " pdb=" OP1 G W 250 " model vdw 1.717 1.850 nonbonded pdb=" O ARG P 108 " pdb=" HG1 THR P 112 " model vdw 1.718 1.850 nonbonded pdb=" OD1 ASP P 91 " pdb=" HZ1 LYS P 136 " model vdw 1.728 1.850 ... (remaining 186892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.160 Extract box with map and model: 2.560 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 55.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.005 0.076 9239 Z= 0.292 Angle : 0.905 7.989 13808 Z= 0.533 Chirality : 0.051 0.261 1722 Planarity : 0.014 0.143 751 Dihedral : 15.852 178.072 4251 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.74 % 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 (0.46), residues: 324 helix: 0.05 (0.48), residues: 95 sheet: 0.92 (0.62), residues: 76 loop : 0.21 (0.51), residues: 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.9476 time to fit residues: 45.0610 Evaluate side-chains 30 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1678 time to fit residues: 0.9401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 9239 Z= 0.191 Angle : 0.592 6.227 13808 Z= 0.324 Chirality : 0.037 0.179 1722 Planarity : 0.005 0.052 751 Dihedral : 15.500 178.779 3587 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 0.37 % 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: 1.00 (0.48), residues: 324 helix: 1.32 (0.51), residues: 98 sheet: 0.37 (0.57), residues: 88 loop : 0.58 (0.58), residues: 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.716 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.8359 time to fit residues: 25.9738 Evaluate side-chains 25 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1522 time to fit residues: 0.9771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 9239 Z= 0.429 Angle : 0.732 7.381 13808 Z= 0.392 Chirality : 0.045 0.269 1722 Planarity : 0.008 0.065 751 Dihedral : 16.098 178.709 3587 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.11 % 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: 0.16 (0.45), residues: 324 helix: 0.77 (0.49), residues: 98 sheet: 0.12 (0.53), residues: 101 loop : -0.27 (0.54), residues: 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.736 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.7639 time to fit residues: 25.9611 Evaluate side-chains 23 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1693 time to fit residues: 1.2766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9239 Z= 0.185 Angle : 0.559 5.266 13808 Z= 0.308 Chirality : 0.035 0.173 1722 Planarity : 0.005 0.038 751 Dihedral : 15.591 178.997 3587 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 1.11 % 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: 0.69 (0.46), residues: 324 helix: 1.66 (0.50), residues: 98 sheet: 0.16 (0.53), residues: 100 loop : -0.12 (0.55), residues: 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.721 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 26 average time/residue: 0.8290 time to fit residues: 26.0363 Evaluate side-chains 23 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.0270 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9239 Z= 0.246 Angle : 0.575 4.836 13808 Z= 0.314 Chirality : 0.036 0.164 1722 Planarity : 0.006 0.039 751 Dihedral : 15.721 179.458 3587 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.11 % 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 (0.46), residues: 324 helix: 1.74 (0.49), residues: 98 sheet: 0.11 (0.52), residues: 105 loop : -0.30 (0.56), residues: 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.684 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.7481 time to fit residues: 22.7451 Evaluate side-chains 23 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1605 time to fit residues: 1.1902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9239 Z= 0.330 Angle : 0.622 5.462 13808 Z= 0.335 Chirality : 0.039 0.190 1722 Planarity : 0.006 0.049 751 Dihedral : 15.987 178.229 3587 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 0.20 (0.46), residues: 324 helix: 1.32 (0.49), residues: 98 sheet: -0.05 (0.51), residues: 105 loop : -0.56 (0.54), residues: 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.686 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.9866 time to fit residues: 24.3451 Evaluate side-chains 21 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 9239 Z= 0.353 Angle : 0.632 5.145 13808 Z= 0.340 Chirality : 0.040 0.177 1722 Planarity : 0.007 0.051 751 Dihedral : 16.115 177.009 3587 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.74 % 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: 0.07 (0.46), residues: 324 helix: 1.28 (0.50), residues: 98 sheet: -0.08 (0.52), residues: 105 loop : -0.76 (0.53), residues: 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.745 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.8854 time to fit residues: 25.4146 Evaluate side-chains 22 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1485 time to fit residues: 0.9067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9239 Z= 0.237 Angle : 0.566 4.958 13808 Z= 0.308 Chirality : 0.036 0.169 1722 Planarity : 0.006 0.059 751 Dihedral : 15.895 177.767 3587 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.37 % 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 (0.46), residues: 324 helix: 1.48 (0.50), residues: 98 sheet: -0.04 (0.52), residues: 100 loop : -0.54 (0.54), residues: 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.741 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.9775 time to fit residues: 28.8541 Evaluate side-chains 24 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 9239 Z= 0.466 Angle : 0.705 5.666 13808 Z= 0.372 Chirality : 0.044 0.198 1722 Planarity : 0.008 0.068 751 Dihedral : 16.365 176.484 3587 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.37 % 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: -0.21 (0.45), residues: 324 helix: 1.00 (0.50), residues: 98 sheet: -0.08 (0.52), residues: 101 loop : -1.01 (0.51), residues: 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.670 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 1.0303 time to fit residues: 27.4930 Evaluate side-chains 22 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 9239 Z= 0.187 Angle : 0.542 4.886 13808 Z= 0.297 Chirality : 0.034 0.162 1722 Planarity : 0.005 0.063 751 Dihedral : 15.847 178.057 3587 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 0.33 (0.47), residues: 324 helix: 1.64 (0.51), residues: 98 sheet: -0.02 (0.53), residues: 100 loop : -0.64 (0.54), residues: 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.769 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.9605 time to fit residues: 29.4556 Evaluate side-chains 24 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113012 restraints weight = 27540.276| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.27 r_work: 0.3088 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9239 Z= 0.186 Angle : 0.526 4.811 13808 Z= 0.288 Chirality : 0.034 0.158 1722 Planarity : 0.005 0.063 751 Dihedral : 15.602 178.593 3587 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 0.53 (0.47), residues: 324 helix: 1.88 (0.51), residues: 98 sheet: 0.05 (0.53), residues: 100 loop : -0.54 (0.55), residues: 126 =============================================================================== Job complete usr+sys time: 3937.71 seconds wall clock time: 70 minutes 15.21 seconds (4215.21 seconds total)