Starting phenix.real_space_refine on Sun Dec 10 20:19:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/12_2023/7uin_26550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/12_2023/7uin_26550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/12_2023/7uin_26550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/12_2023/7uin_26550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/12_2023/7uin_26550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/12_2023/7uin_26550_updated.pdb" } resolution = 2.8 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= 0.034 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 578 5.49 5 Mg 28 5.21 5 S 21 5.16 5 C 7546 2.51 5 N 2869 2.21 5 O 4543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D ASP 376": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15585 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 11639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 11639 Classifications: {'RNA': 541} Modifications used: {'rna2p_pur': 38, 'rna2p_pyr': 10, 'rna3p_pur': 290, 'rna3p_pyr': 203} Link IDs: {'rna2p': 47, 'rna3p': 493} Chain breaks: 5 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 759 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 28, 'NH4': 2} Classifications: {'undetermined': 30, 'water': 23} Link IDs: {None: 52} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.84, per 1000 atoms: 0.57 Number of scatterers: 15585 At special positions: 0 Unit cell: (99.008, 158.08, 158.08, 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 21 16.00 P 578 15.00 Mg 28 11.99 O 4543 8.00 N 2869 7.00 C 7546 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: 9.29 Conformation dependent library (CDL) restraints added in 689.6 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 61.8% alpha, 5.9% beta 205 base pairs and 342 stacking pairs defined. Time for finding SS restraints: 10.29 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 39 through 56 removed outlier: 6.802A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 Proline residue: D 100 - end of helix Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 145 through 148 No H-bonds generated for 'chain 'D' and resid 145 through 148' Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.917A pdb=" N LEU D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 251 Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 314 through 332 Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 416 through 423 Processing sheet with id= A, first strand: chain 'D' and resid 263 through 265 removed outlier: 3.948A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 275 through 279 169 hydrogen bonds defined for protein. 501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 501 hydrogen bonds 792 hydrogen bond angles 0 basepair planarities 205 basepair parallelities 342 stacking parallelities Total time for adding SS restraints: 9.26 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.13: 1 1.13 - 1.43: 9395 1.43 - 1.73: 7647 1.73 - 2.04: 34 2.04 - 2.34: 1 Bond restraints: 17078 Sorted by residual: bond pdb=" CG PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 1.503 0.828 0.675 3.40e-02 8.65e+02 3.95e+02 bond pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " ideal model delta sigma weight residual 1.492 2.337 -0.845 5.00e-02 4.00e+02 2.86e+02 bond pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 1.473 1.595 -0.122 1.40e-02 5.10e+03 7.65e+01 bond pdb=" N PRO D 281 " pdb=" CA PRO D 281 " ideal model delta sigma weight residual 1.471 1.397 0.074 1.32e-02 5.74e+03 3.15e+01 bond pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " ideal model delta sigma weight residual 1.534 1.462 0.072 1.40e-02 5.10e+03 2.63e+01 ... (remaining 17073 not shown) Histogram of bond angle deviations from ideal: 0.08 - 29.81: 1 29.81 - 59.54: 0 59.54 - 89.28: 0 89.28 - 119.01: 17403 119.01 - 148.74: 8514 Bond angle restraints: 25918 Sorted by residual: angle pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 106.10 0.08 106.02 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 112.00 89.42 22.58 1.40e+00 5.10e-01 2.60e+02 angle pdb=" N PRO D 281 " pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " ideal model delta sigma weight residual 103.48 89.59 13.89 1.00e+00 1.00e+00 1.93e+02 angle pdb=" CA PRO D 62 " pdb=" N PRO D 62 " pdb=" CD PRO D 62 " ideal model delta sigma weight residual 112.00 94.92 17.08 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO D 281 " pdb=" CB PRO D 281 " pdb=" CG PRO D 281 " ideal model delta sigma weight residual 104.50 90.46 14.04 1.90e+00 2.77e-01 5.46e+01 ... (remaining 25913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 8754 35.84 - 71.68: 1279 71.68 - 107.51: 157 107.51 - 143.35: 8 143.35 - 179.19: 10 Dihedral angle restraints: 10208 sinusoidal: 9084 harmonic: 1124 Sorted by residual: dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 46.39 153.61 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 200.00 48.62 151.38 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' C B 440 " pdb=" C1' C B 440 " pdb=" N1 C B 440 " pdb=" C2 C B 440 " ideal model delta sinusoidal sigma weight residual 232.00 79.74 152.26 1 1.70e+01 3.46e-03 6.26e+01 ... (remaining 10205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3113 0.087 - 0.175: 179 0.175 - 0.262: 14 0.262 - 0.350: 9 0.350 - 0.437: 3 Chirality restraints: 3318 Sorted by residual: chirality pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" C PRO D 281 " pdb=" CB PRO D 281 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE D 168 " pdb=" CA ILE D 168 " pdb=" CG1 ILE D 168 " pdb=" CG2 ILE D 168 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C1' A B 370 " pdb=" O4' A B 370 " pdb=" C2' A B 370 " pdb=" N9 A B 370 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3315 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 47 " 0.032 2.00e-02 2.50e+03 6.26e-02 3.92e+01 pdb=" CG ASN D 47 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 47 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 47 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 258 " 0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" CG ASN D 258 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN D 258 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN D 258 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 61 " -0.078 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO D 62 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " -0.058 5.00e-02 4.00e+02 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 11 2.16 - 2.85: 4627 2.85 - 3.53: 21507 3.53 - 4.22: 52724 4.22 - 4.90: 65838 Nonbonded interactions: 144707 Sorted by model distance: nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 1.477 2.170 nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.870 2.170 nonbonded pdb=" OP2 A B 559 " pdb="MG MG B 703 " model vdw 2.041 2.170 nonbonded pdb=" OP1 G B 247 " pdb="MG MG B 705 " model vdw 2.056 2.170 nonbonded pdb=" OP2 A B 157 " pdb="MG MG B 708 " model vdw 2.080 2.170 ... (remaining 144702 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: 3.820 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: 12.750 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 54.820 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.010 0.845 17078 Z= 0.690 Angle : 1.206 106.017 25918 Z= 0.554 Chirality : 0.047 0.437 3318 Planarity : 0.009 0.108 1121 Dihedral : 24.954 179.187 9484 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 2.93 % Allowed : 36.36 % Favored : 60.70 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.37), residues: 381 helix: -0.53 (0.28), residues: 253 sheet: 0.31 (0.92), residues: 24 loop : -1.20 (0.56), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 357 HIS 0.016 0.004 HIS D 43 PHE 0.021 0.005 PHE D 298 TYR 0.029 0.003 TYR D 385 ARG 0.009 0.001 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.740 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 1.3812 time to fit residues: 90.0707 Evaluate side-chains 40 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 1.2289 time to fit residues: 2.0499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 17078 Z= 0.243 Angle : 0.657 7.535 25918 Z= 0.340 Chirality : 0.035 0.251 3318 Planarity : 0.007 0.142 1121 Dihedral : 24.802 177.856 8679 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 7.62 % Allowed : 31.96 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.40), residues: 381 helix: 0.45 (0.30), residues: 257 sheet: 0.52 (0.95), residues: 24 loop : -0.96 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 357 HIS 0.005 0.001 HIS D 284 PHE 0.018 0.002 PHE D 298 TYR 0.023 0.002 TYR D 385 ARG 0.008 0.001 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 40 time to evaluate : 0.672 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 62 average time/residue: 1.3168 time to fit residues: 90.3632 Evaluate side-chains 43 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1333 time to fit residues: 0.9574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17078 Z= 0.213 Angle : 0.625 8.471 25918 Z= 0.324 Chirality : 0.034 0.245 3318 Planarity : 0.006 0.143 1121 Dihedral : 24.714 179.210 8679 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 7.04 % Allowed : 31.96 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.59 (0.41), residues: 381 helix: 0.90 (0.30), residues: 260 sheet: 0.58 (0.91), residues: 24 loop : -0.85 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 PHE 0.013 0.002 PHE D 298 TYR 0.022 0.002 TYR D 385 ARG 0.004 0.001 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 38 time to evaluate : 0.711 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 60 average time/residue: 1.2457 time to fit residues: 83.5288 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.2118 time to fit residues: 1.4151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17078 Z= 0.161 Angle : 0.593 7.553 25918 Z= 0.308 Chirality : 0.032 0.219 3318 Planarity : 0.006 0.138 1121 Dihedral : 24.709 179.691 8679 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 6.16 % Allowed : 33.43 % Favored : 60.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % 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: 0.98 (0.41), residues: 381 helix: 1.22 (0.31), residues: 260 sheet: 0.70 (0.94), residues: 24 loop : -0.77 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 357 HIS 0.004 0.001 HIS D 43 PHE 0.009 0.002 PHE D 298 TYR 0.019 0.001 TYR D 385 ARG 0.005 0.000 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.754 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 60 average time/residue: 1.2945 time to fit residues: 86.6082 Evaluate side-chains 47 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1521 time to fit residues: 1.2596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 0.0370 chunk 37 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 overall best weight: 1.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17078 Z= 0.272 Angle : 0.669 7.755 25918 Z= 0.347 Chirality : 0.037 0.260 3318 Planarity : 0.006 0.131 1121 Dihedral : 24.721 177.520 8679 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 7.92 % Allowed : 31.96 % Favored : 60.12 % 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: 0.65 (0.41), residues: 381 helix: 0.95 (0.30), residues: 260 sheet: 1.02 (0.97), residues: 24 loop : -0.98 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.014 0.002 PHE D 298 TYR 0.028 0.002 TYR D 385 ARG 0.003 0.001 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 39 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 62 average time/residue: 1.1784 time to fit residues: 81.8087 Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.6458 time to fit residues: 2.1921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17078 Z= 0.272 Angle : 0.658 9.801 25918 Z= 0.342 Chirality : 0.036 0.233 3318 Planarity : 0.006 0.127 1121 Dihedral : 24.666 178.141 8679 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.99 % Allowed : 34.60 % Favored : 60.41 % 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: 0.58 (0.41), residues: 381 helix: 0.93 (0.30), residues: 260 sheet: 0.85 (0.98), residues: 24 loop : -1.06 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.011 0.002 PHE D 298 TYR 0.025 0.002 TYR D 385 ARG 0.003 0.001 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 38 time to evaluate : 0.790 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 52 average time/residue: 1.1507 time to fit residues: 67.7407 Evaluate side-chains 49 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.6449 time to fit residues: 2.2259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17078 Z= 0.254 Angle : 0.643 9.367 25918 Z= 0.334 Chirality : 0.036 0.235 3318 Planarity : 0.007 0.135 1121 Dihedral : 24.638 177.681 8679 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.40 % Allowed : 34.31 % Favored : 61.29 % 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: 0.67 (0.42), residues: 381 helix: 1.01 (0.31), residues: 260 sheet: 0.87 (0.98), residues: 24 loop : -1.09 (0.65), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 PHE 0.013 0.002 PHE D 298 TYR 0.026 0.002 TYR D 385 ARG 0.018 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.714 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 54 average time/residue: 1.1459 time to fit residues: 69.6412 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1790 time to fit residues: 0.9949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.0470 chunk 80 optimal weight: 0.4980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17078 Z= 0.162 Angle : 0.609 10.927 25918 Z= 0.318 Chirality : 0.032 0.224 3318 Planarity : 0.006 0.122 1121 Dihedral : 24.647 178.283 8679 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.11 % Allowed : 35.19 % Favored : 60.70 % 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: 0.81 (0.42), residues: 381 helix: 1.17 (0.31), residues: 257 sheet: 0.48 (0.99), residues: 24 loop : -0.97 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 357 HIS 0.002 0.001 HIS D 109 PHE 0.012 0.002 PHE D 298 TYR 0.017 0.001 TYR D 385 ARG 0.011 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.681 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 51 average time/residue: 1.1808 time to fit residues: 67.8633 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2208 time to fit residues: 1.0552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17078 Z= 0.180 Angle : 0.603 10.572 25918 Z= 0.314 Chirality : 0.032 0.225 3318 Planarity : 0.006 0.121 1121 Dihedral : 24.598 178.739 8679 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 4.40 % Allowed : 34.90 % Favored : 60.70 % 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: 0.96 (0.43), residues: 381 helix: 1.29 (0.32), residues: 260 sheet: 0.30 (0.95), residues: 24 loop : -0.95 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 357 HIS 0.002 0.001 HIS D 109 PHE 0.012 0.002 PHE D 298 TYR 0.020 0.001 TYR D 385 ARG 0.004 0.000 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.770 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 1.1134 time to fit residues: 66.7072 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1966 time to fit residues: 1.0128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17078 Z= 0.230 Angle : 0.629 11.039 25918 Z= 0.327 Chirality : 0.034 0.231 3318 Planarity : 0.006 0.120 1121 Dihedral : 24.553 178.251 8679 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 4.11 % Allowed : 35.48 % Favored : 60.41 % 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: 0.80 (0.43), residues: 381 helix: 1.15 (0.31), residues: 260 sheet: 0.24 (0.95), residues: 24 loop : -0.97 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.007 0.002 HIS D 43 PHE 0.014 0.002 PHE D 298 TYR 0.025 0.002 TYR D 385 ARG 0.003 0.000 ARG D 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 50 average time/residue: 1.1692 time to fit residues: 65.5481 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1917 time to fit residues: 0.9997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.0070 chunk 4 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.194956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151665 restraints weight = 20013.417| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.01 r_work: 0.3473 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17078 Z= 0.393 Angle : 0.768 11.386 25918 Z= 0.394 Chirality : 0.043 0.272 3318 Planarity : 0.007 0.119 1121 Dihedral : 24.692 178.188 8679 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Rotamer: Outliers : 3.23 % Allowed : 36.66 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.42), residues: 381 helix: 0.65 (0.31), residues: 260 sheet: 0.81 (1.24), residues: 14 loop : -1.20 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP D 357 HIS 0.006 0.002 HIS D 109 PHE 0.021 0.003 PHE D 298 TYR 0.031 0.003 TYR D 385 ARG 0.004 0.001 ARG D 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3074.14 seconds wall clock time: 56 minutes 58.45 seconds (3418.45 seconds total)