Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:07:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/04_2023/8g8e_29846.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/04_2023/8g8e_29846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/04_2023/8g8e_29846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/04_2023/8g8e_29846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/04_2023/8g8e_29846.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8e_29846/04_2023/8g8e_29846.pdb" } resolution = 4.2 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 64 5.49 5 S 5 5.16 5 C 1357 2.51 5 N 453 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 2464 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 661 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 651 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 2.07, per 1000 atoms: 0.84 Number of scatterers: 2464 At special positions: 0 Unit cell: (69.96, 76.32, 115.54, 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 5 16.00 P 64 15.00 O 585 8.00 N 453 7.00 C 1357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 185.8 milliseconds 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 266 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.4% alpha, 0.0% beta 31 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.554A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 238 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 471 1.33 - 1.45: 884 1.45 - 1.57: 1149 1.57 - 1.69: 126 1.69 - 1.81: 6 Bond restraints: 2636 Sorted by residual: bond pdb=" CG LEU X 200 " pdb=" CD1 LEU X 200 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" C3' DC I 75 " pdb=" C2' DC I 75 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.98e-01 bond pdb=" CB MET X 197 " pdb=" CG MET X 197 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.79e-01 ... (remaining 2631 not shown) Histogram of bond angle deviations from ideal: 97.55 - 104.83: 253 104.83 - 112.11: 1443 112.11 - 119.39: 839 119.39 - 126.67: 1075 126.67 - 133.96: 212 Bond angle restraints: 3822 Sorted by residual: angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.61 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA GLU X 238 " pdb=" CB GLU X 238 " pdb=" CG GLU X 238 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C3' DT J -88 " pdb=" C2' DT J -88 " pdb=" C1' DT J -88 " ideal model delta sigma weight residual 101.60 97.55 4.05 1.50e+00 4.44e-01 7.31e+00 angle pdb=" CA MET X 197 " pdb=" CB MET X 197 " pdb=" CG MET X 197 " ideal model delta sigma weight residual 114.10 119.03 -4.93 2.00e+00 2.50e-01 6.08e+00 angle pdb=" CA LEU X 200 " pdb=" CB LEU X 200 " pdb=" CG LEU X 200 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 ... (remaining 3817 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 30.43: 1023 30.43 - 60.84: 336 60.84 - 91.26: 2 91.26 - 121.68: 0 121.68 - 152.10: 2 Dihedral angle restraints: 1363 sinusoidal: 958 harmonic: 405 Sorted by residual: dihedral pdb=" C4' DA I 74 " pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " pdb=" P DC I 75 " ideal model delta sinusoidal sigma weight residual 220.00 67.90 152.10 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.85 138.15 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU X 238 " pdb=" C GLU X 238 " pdb=" N ASN X 239 " pdb=" CA ASN X 239 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 283 0.030 - 0.060: 109 0.060 - 0.089: 26 0.089 - 0.119: 8 0.119 - 0.149: 4 Chirality restraints: 430 Sorted by residual: chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA LEU X 267 " pdb=" N LEU X 267 " pdb=" C LEU X 267 " pdb=" CB LEU X 267 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CG LEU X 217 " pdb=" CB LEU X 217 " pdb=" CD1 LEU X 217 " pdb=" CD2 LEU X 217 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 427 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 254 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO X 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -80 " -0.019 2.00e-02 2.50e+03 9.43e-03 2.00e+00 pdb=" N1 DC J -80 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC J -80 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC J -80 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J -80 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J -80 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC J -80 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 277 " -0.011 2.00e-02 2.50e+03 8.31e-03 1.72e+00 pdb=" CG TRP X 277 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP X 277 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 277 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 277 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 277 " -0.000 2.00e-02 2.50e+03 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 531 2.80 - 3.33: 2248 3.33 - 3.85: 4846 3.85 - 4.38: 5302 4.38 - 4.90: 7197 Nonbonded interactions: 20124 Sorted by model distance: nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.277 2.440 nonbonded pdb=" OP2 DA J -87 " pdb=" ND2 ASN X 196 " model vdw 2.302 2.520 nonbonded pdb=" NE ARG X 157 " pdb=" OE2 GLU X 188 " model vdw 2.303 2.520 nonbonded pdb=" NH2 ARG X 157 " pdb=" OE1 GLU X 188 " model vdw 2.305 2.520 nonbonded pdb=" O LEU X 248 " pdb=" NE2 GLN X 251 " model vdw 2.308 2.520 ... (remaining 20119 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 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: 0.580 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: 2.980 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 : 0.004 0.037 2636 Z= 0.239 Angle : 0.730 11.907 3822 Z= 0.409 Chirality : 0.036 0.149 430 Planarity : 0.005 0.041 263 Dihedral : 28.648 152.096 1097 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 0.79 % 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: 0.35 (0.74), residues: 136 helix: 0.74 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.73 (1.21), residues: 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.2327 time to fit residues: 11.8791 Evaluate side-chains 26 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0531 time to fit residues: 0.2969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2636 Z= 0.193 Angle : 0.596 4.809 3822 Z= 0.358 Chirality : 0.032 0.106 430 Planarity : 0.005 0.050 263 Dihedral : 31.394 148.639 785 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.57 (0.74), residues: 136 helix: 0.90 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.66 (1.19), residues: 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1789 time to fit residues: 5.8811 Evaluate side-chains 22 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 2636 Z= 0.199 Angle : 0.598 6.647 3822 Z= 0.359 Chirality : 0.032 0.144 430 Planarity : 0.004 0.029 263 Dihedral : 31.555 148.445 785 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 0.73 (0.73), residues: 136 helix: 1.01 (0.51), residues: 111 sheet: None (None), residues: 0 loop : -1.68 (1.06), residues: 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1424 time to fit residues: 4.3763 Evaluate side-chains 19 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2636 Z= 0.214 Angle : 0.608 5.628 3822 Z= 0.367 Chirality : 0.032 0.126 430 Planarity : 0.004 0.022 263 Dihedral : 31.629 149.022 785 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.13 (0.70), residues: 136 helix: 0.48 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.29 (0.99), residues: 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1505 time to fit residues: 4.0655 Evaluate side-chains 19 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2636 Z= 0.174 Angle : 0.581 5.373 3822 Z= 0.348 Chirality : 0.032 0.139 430 Planarity : 0.003 0.017 263 Dihedral : 31.588 149.641 785 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.39 (0.70), residues: 136 helix: 0.66 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.10 (0.94), residues: 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1497 time to fit residues: 4.5863 Evaluate side-chains 17 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.6986 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2636 Z= 0.191 Angle : 0.629 5.863 3822 Z= 0.378 Chirality : 0.035 0.134 430 Planarity : 0.003 0.017 263 Dihedral : 31.551 149.686 785 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.05 (0.69), residues: 136 helix: 0.42 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -1.19 (0.90), residues: 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1518 time to fit residues: 4.2828 Evaluate side-chains 16 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.6967 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2636 Z= 0.182 Angle : 0.616 5.476 3822 Z= 0.375 Chirality : 0.034 0.144 430 Planarity : 0.003 0.023 263 Dihedral : 31.560 149.872 785 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -0.07 (0.70), residues: 136 helix: 0.31 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.19 (0.91), residues: 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.215 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1475 time to fit residues: 4.2131 Evaluate side-chains 17 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.6955 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2636 Z= 0.175 Angle : 0.617 5.661 3822 Z= 0.374 Chirality : 0.035 0.160 430 Planarity : 0.003 0.020 263 Dihedral : 31.574 150.027 785 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -0.26 (0.70), residues: 136 helix: 0.22 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.44 (0.87), residues: 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.201 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1463 time to fit residues: 4.1362 Evaluate side-chains 16 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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: 0.6991 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2636 Z= 0.183 Angle : 0.604 5.876 3822 Z= 0.367 Chirality : 0.033 0.139 430 Planarity : 0.003 0.018 263 Dihedral : 31.620 150.271 785 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -0.14 (0.71), residues: 136 helix: 0.28 (0.51), residues: 111 sheet: None (None), residues: 0 loop : -1.30 (0.91), residues: 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.217 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1340 time to fit residues: 3.5068 Evaluate side-chains 16 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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: 0.7075 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 2636 Z= 0.232 Angle : 0.642 6.947 3822 Z= 0.385 Chirality : 0.035 0.146 430 Planarity : 0.004 0.022 263 Dihedral : 31.780 150.292 785 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -0.40 (0.70), residues: 136 helix: 0.09 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.33 (0.94), residues: 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1411 time to fit residues: 4.3684 Evaluate side-chains 18 residues out of total 127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 = 0.2729 r_free = 0.2729 target = 0.027739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.021257 restraints weight = 33229.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.022242 restraints weight = 15220.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.022890 restraints weight = 9033.335| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2636 Z= 0.177 Angle : 0.611 6.320 3822 Z= 0.369 Chirality : 0.033 0.153 430 Planarity : 0.003 0.018 263 Dihedral : 31.843 149.787 785 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -0.22 (0.71), residues: 136 helix: 0.23 (0.51), residues: 111 sheet: None (None), residues: 0 loop : -1.36 (0.95), residues: 25 =============================================================================== Job complete usr+sys time: 887.48 seconds wall clock time: 16 minutes 30.38 seconds (990.38 seconds total)