Starting phenix.real_space_refine on Tue Nov 14 01:14:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/11_2023/7uo2_26638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/11_2023/7uo2_26638.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/7uo2_26638/11_2023/7uo2_26638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/11_2023/7uo2_26638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/11_2023/7uo2_26638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo2_26638/11_2023/7uo2_26638.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 270 5.49 5 Mg 3 5.21 5 S 2 5.16 5 C 3171 2.51 5 N 1258 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6735 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 5813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 5813 Unusual residues: {' MG': 3} Classifications: {'RNA': 271, 'undetermined': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 29, 'rna2p_pyr': 26, 'rna3p_pur': 122, 'rna3p_pyr': 94} Link IDs: {'rna2p': 55, 'rna3p': 215, None: 3} Not linked: pdbres=" U B 376 " pdbres=" MG B 401 " Not linked: pdbres=" MG B 401 " pdbres=" MG B 402 " Not linked: pdbres=" MG B 402 " pdbres=" MG B 403 " Chain breaks: 1 Time building chain proxies: 4.33, per 1000 atoms: 0.64 Number of scatterers: 6735 At special positions: 0 Unit cell: (88.5636, 124.96, 127.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 2 16.00 P 270 15.00 Mg 3 11.99 O 2031 8.00 N 1258 7.00 C 3171 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: 3.89 Conformation dependent library (CDL) restraints added in 231.9 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 214 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 40.2% alpha, 9.8% beta 81 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.850A pdb=" N LEU A 9 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 13 through 23 removed outlier: 4.134A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.956A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.504A pdb=" N LEU A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.850A pdb=" N THR A 33 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 87 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A 45 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 86 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 218 hydrogen bonds 400 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 570 1.32 - 1.44: 3614 1.44 - 1.56: 2714 1.56 - 1.69: 539 1.69 - 1.81: 3 Bond restraints: 7440 Sorted by residual: bond pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sigma weight residual 1.529 1.508 0.021 1.50e-02 4.44e+03 1.88e+00 bond pdb=" C4' U B 17 " pdb=" C3' U B 17 " ideal model delta sigma weight residual 1.521 1.540 -0.019 1.50e-02 4.44e+03 1.62e+00 bond pdb=" O3' U B 17 " pdb=" P C B 18 " ideal model delta sigma weight residual 1.607 1.624 -0.017 1.50e-02 4.44e+03 1.31e+00 bond pdb=" O4' G B 271 " pdb=" C1' G B 271 " ideal model delta sigma weight residual 1.412 1.429 -0.017 1.50e-02 4.44e+03 1.23e+00 bond pdb=" C4' G B 271 " pdb=" C3' G B 271 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.50e-02 4.44e+03 1.17e+00 ... (remaining 7435 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.92: 1458 105.92 - 112.92: 4320 112.92 - 119.93: 2689 119.93 - 126.93: 2266 126.93 - 133.93: 667 Bond angle restraints: 11400 Sorted by residual: angle pdb=" C2' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 112.00 106.53 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" O3' U B 17 " ideal model delta sigma weight residual 113.00 117.92 -4.92 1.50e+00 4.44e-01 1.08e+01 angle pdb=" O4' G B 271 " pdb=" C4' G B 271 " pdb=" C3' G B 271 " ideal model delta sigma weight residual 104.00 100.99 3.01 1.00e+00 1.00e+00 9.05e+00 angle pdb=" C4' G B 271 " pdb=" C3' G B 271 " pdb=" O3' G B 271 " ideal model delta sigma weight residual 113.00 117.45 -4.45 1.50e+00 4.44e-01 8.78e+00 angle pdb=" O4' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 108.50 112.90 -4.40 1.50e+00 4.44e-01 8.59e+00 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 3527 35.14 - 70.28: 273 70.28 - 105.41: 24 105.41 - 140.55: 4 140.55 - 175.69: 4 Dihedral angle restraints: 3832 sinusoidal: 3507 harmonic: 325 Sorted by residual: dihedral pdb=" O4' U B 257 " pdb=" C1' U B 257 " pdb=" N1 U B 257 " pdb=" C2 U B 257 " ideal model delta sinusoidal sigma weight residual 200.00 51.23 148.77 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U B 331 " pdb=" C1' U B 331 " pdb=" N1 U B 331 " pdb=" C2 U B 331 " ideal model delta sinusoidal sigma weight residual -128.00 47.69 -175.69 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U B 302 " pdb=" C1' U B 302 " pdb=" N1 U B 302 " pdb=" C2 U B 302 " ideal model delta sinusoidal sigma weight residual 232.00 58.14 173.86 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1424 0.058 - 0.116: 58 0.116 - 0.174: 9 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 1493 Sorted by residual: chirality pdb=" C3' G B 271 " pdb=" C4' G B 271 " pdb=" O3' G B 271 " pdb=" C2' G B 271 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1' G B 16 " pdb=" O4' G B 16 " pdb=" C2' G B 16 " pdb=" N9 G B 16 " both_signs ideal model delta sigma weight residual False 2.46 2.66 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1' G B 324 " pdb=" O4' G B 324 " pdb=" C2' G B 324 " pdb=" N9 G B 324 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 1490 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 271 " 0.053 2.00e-02 2.50e+03 2.45e-02 1.81e+01 pdb=" N9 G B 271 " -0.064 2.00e-02 2.50e+03 pdb=" C8 G B 271 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 271 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 271 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 271 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B 271 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G B 271 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 271 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 271 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 271 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G B 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 17 " 0.015 2.00e-02 2.50e+03 2.20e-02 1.09e+01 pdb=" N1 U B 17 " 0.014 2.00e-02 2.50e+03 pdb=" C2 U B 17 " -0.028 2.00e-02 2.50e+03 pdb=" O2 U B 17 " -0.013 2.00e-02 2.50e+03 pdb=" N3 U B 17 " 0.037 2.00e-02 2.50e+03 pdb=" C4 U B 17 " -0.029 2.00e-02 2.50e+03 pdb=" O4 U B 17 " 0.021 2.00e-02 2.50e+03 pdb=" C5 U B 17 " -0.018 2.00e-02 2.50e+03 pdb=" C6 U B 17 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 16 " -0.042 2.00e-02 2.50e+03 1.73e-02 8.95e+00 pdb=" N9 G B 16 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G B 16 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G B 16 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 16 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 16 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G B 16 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G B 16 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 16 " 0.014 2.00e-02 2.50e+03 pdb=" N2 G B 16 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G B 16 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G B 16 " 0.007 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 175 2.61 - 3.18: 5207 3.18 - 3.75: 13421 3.75 - 4.33: 16769 4.33 - 4.90: 22869 Nonbonded interactions: 58441 Sorted by model distance: nonbonded pdb=" OP1 G B 250 " pdb="MG MG B 403 " model vdw 2.033 2.170 nonbonded pdb=" OP1 A B 67 " pdb="MG MG B 401 " model vdw 2.049 2.170 nonbonded pdb=" OP1 A B 351 " pdb="MG MG B 401 " model vdw 2.066 2.170 nonbonded pdb=" O2' A B 112 " pdb=" OP1 C B 115 " model vdw 2.134 2.440 nonbonded pdb=" O2' G B 262 " pdb=" OP1 U B 263 " model vdw 2.221 2.440 ... (remaining 58436 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: 4.310 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: 0.010 Extract box with map and model: 10.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7440 Z= 0.115 Angle : 0.549 7.444 11400 Z= 0.273 Chirality : 0.027 0.290 1493 Planarity : 0.004 0.035 435 Dihedral : 19.036 175.688 3618 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Rotamer: Outliers : 2.04 % Allowed : 10.20 % Favored : 87.76 % 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: -3.16 (0.70), residues: 110 helix: -0.20 (0.84), residues: 36 sheet: -1.26 (1.44), residues: 14 loop : -3.74 (0.58), residues: 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.316 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.2612 time to fit residues: 9.8893 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 7440 Z= 0.390 Angle : 0.914 7.427 11400 Z= 0.456 Chirality : 0.046 0.261 1493 Planarity : 0.007 0.037 435 Dihedral : 20.455 175.476 3373 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 4.08 % Allowed : 14.29 % Favored : 81.63 % 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: -3.47 (0.69), residues: 110 helix: -0.99 (0.79), residues: 39 sheet: -1.67 (1.24), residues: 14 loop : -3.57 (0.65), residues: 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.280 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.2834 time to fit residues: 8.4223 Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0559 time to fit residues: 0.4170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 7440 Z= 0.491 Angle : 1.008 7.790 11400 Z= 0.492 Chirality : 0.051 0.275 1493 Planarity : 0.008 0.039 435 Dihedral : 21.468 171.063 3373 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 35.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer: Outliers : 4.08 % Allowed : 17.35 % Favored : 78.57 % 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: -3.45 (0.72), residues: 110 helix: -1.53 (0.74), residues: 40 sheet: -1.51 (1.18), residues: 14 loop : -3.16 (0.79), residues: 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.291 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.3337 time to fit residues: 8.9331 Evaluate side-chains 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0632 time to fit residues: 0.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7440 Z= 0.381 Angle : 0.879 7.793 11400 Z= 0.434 Chirality : 0.045 0.254 1493 Planarity : 0.007 0.040 435 Dihedral : 21.115 172.151 3373 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 5.10 % Allowed : 19.39 % Favored : 75.51 % 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: -3.12 (0.77), residues: 110 helix: -1.18 (0.79), residues: 40 sheet: -1.38 (1.14), residues: 14 loop : -3.01 (0.84), residues: 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.291 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.2939 time to fit residues: 9.0606 Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0623 time to fit residues: 0.4661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 7440 Z= 0.409 Angle : 0.918 7.869 11400 Z= 0.452 Chirality : 0.047 0.256 1493 Planarity : 0.007 0.050 435 Dihedral : 21.294 171.702 3373 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 31.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Rotamer: Outliers : 6.12 % Allowed : 20.41 % Favored : 73.47 % 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: -3.69 (0.72), residues: 110 helix: -1.72 (0.73), residues: 46 sheet: -1.90 (1.06), residues: 14 loop : -3.34 (0.80), residues: 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.306 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 25 average time/residue: 0.2553 time to fit residues: 8.1958 Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0640 time to fit residues: 0.4794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7440 Z= 0.352 Angle : 0.860 7.681 11400 Z= 0.425 Chirality : 0.044 0.273 1493 Planarity : 0.006 0.046 435 Dihedral : 21.174 172.369 3373 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 5.10 % Allowed : 20.41 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.78), residues: 110 helix: -0.95 (0.84), residues: 40 sheet: -1.57 (1.10), residues: 14 loop : -2.79 (0.84), residues: 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.293 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.2512 time to fit residues: 8.0210 Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0746 time to fit residues: 0.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7440 Z= 0.409 Angle : 0.933 7.723 11400 Z= 0.459 Chirality : 0.047 0.286 1493 Planarity : 0.008 0.065 435 Dihedral : 21.352 171.792 3373 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 32.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer: Outliers : 4.08 % Allowed : 23.47 % Favored : 72.45 % 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: -3.60 (0.73), residues: 110 helix: -1.69 (0.75), residues: 46 sheet: -1.54 (1.02), residues: 14 loop : -3.35 (0.82), residues: 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.320 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 0.2171 time to fit residues: 6.6988 Evaluate side-chains 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0729 time to fit residues: 0.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 7440 Z= 0.463 Angle : 1.009 8.505 11400 Z= 0.494 Chirality : 0.051 0.291 1493 Planarity : 0.008 0.055 435 Dihedral : 21.691 171.325 3373 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 35.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.27 % Favored : 82.73 % Rotamer: Outliers : 4.08 % Allowed : 24.49 % Favored : 71.43 % 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: -3.08 (0.79), residues: 110 helix: -1.25 (0.84), residues: 40 sheet: -1.52 (1.01), residues: 14 loop : -2.86 (0.87), residues: 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.298 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.2190 time to fit residues: 6.4127 Evaluate side-chains 21 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0623 time to fit residues: 0.4678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7440 Z= 0.333 Angle : 0.859 7.396 11400 Z= 0.424 Chirality : 0.044 0.278 1493 Planarity : 0.006 0.045 435 Dihedral : 21.228 172.421 3373 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 27.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.80), residues: 110 helix: -1.02 (0.85), residues: 40 sheet: -1.37 (0.94), residues: 14 loop : -2.67 (0.89), residues: 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1765 time to fit residues: 4.8774 Evaluate side-chains 18 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7440 Z= 0.276 Angle : 0.805 7.195 11400 Z= 0.399 Chirality : 0.041 0.278 1493 Planarity : 0.006 0.043 435 Dihedral : 20.948 173.711 3373 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 0.00 % Allowed : 30.61 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.81), residues: 110 helix: -0.85 (0.87), residues: 40 sheet: -1.34 (0.98), residues: 14 loop : -2.54 (0.89), residues: 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1885 time to fit residues: 4.9157 Evaluate side-chains 19 residues out of total 98 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.059229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.045835 restraints weight = 55668.250| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.82 r_work: 0.3324 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 7440 Z= 0.510 Angle : 1.054 9.258 11400 Z= 0.512 Chirality : 0.052 0.290 1493 Planarity : 0.008 0.063 435 Dihedral : 21.650 171.379 3373 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 38.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 4.08 % Allowed : 26.53 % Favored : 69.39 % 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: -3.08 (0.79), residues: 110 helix: -1.33 (0.83), residues: 40 sheet: -1.34 (0.99), residues: 14 loop : -2.83 (0.88), residues: 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1416.92 seconds wall clock time: 29 minutes 0.29 seconds (1740.29 seconds total)