Starting phenix.real_space_refine on Fri Feb 16 13:41:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2024/7uin_26550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2024/7uin_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_26550/02_2024/7uin_26550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2024/7uin_26550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2024/7uin_26550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uin_26550/02_2024/7uin_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-dev-5238/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: 9.10, per 1000 atoms: 0.58 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: 9.38 Conformation dependent library (CDL) restraints added in 821.9 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: 11.98 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: 9.16 Time building geometry restraints manager: 9.82 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: 9034 35.84 - 71.68: 1447 71.68 - 107.51: 157 107.51 - 143.35: 8 143.35 - 179.19: 10 Dihedral angle restraints: 10656 sinusoidal: 9532 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 10653 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: 8.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.130 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 58.580 Find NCS groups from input model: 0.280 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.810 ------------------------------------------------------------------------------- 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 : 25.610 179.187 9932 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 : 0.766 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 1.3542 time to fit residues: 88.5778 Evaluate side-chains 40 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.9980 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: 9.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17078 Z= 0.249 Angle : 0.663 8.013 25918 Z= 0.343 Chirality : 0.036 0.259 3318 Planarity : 0.007 0.142 1121 Dihedral : 25.515 177.557 9140 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 7.04 % Allowed : 32.55 % 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: -0.01 (0.39), residues: 381 helix: 0.40 (0.29), residues: 257 sheet: 0.44 (0.93), residues: 24 loop : -0.92 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.018 0.002 PHE D 298 TYR 0.024 0.002 TYR D 385 ARG 0.006 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 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 40 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: D 236 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5453 (ttt) REVERT: D 270 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7502 (tp) REVERT: D 358 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8666 (tptp) outliers start: 24 outliers final: 5 residues processed: 60 average time/residue: 1.3271 time to fit residues: 87.8738 Evaluate side-chains 43 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS 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: 0.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.1952 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= 0.214 Angle : 0.631 8.207 25918 Z= 0.326 Chirality : 0.034 0.247 3318 Planarity : 0.006 0.142 1121 Dihedral : 25.408 179.188 9134 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 7.92 % Allowed : 30.50 % Favored : 61.58 % 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: 0.89 (0.30), residues: 260 sheet: 0.65 (0.93), 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 0.023 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 68 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 41 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 219 LEU cc_start: 0.6852 (mm) cc_final: 0.6628 (mt) REVERT: D 226 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6753 (p0) outliers start: 27 outliers final: 10 residues processed: 63 average time/residue: 1.2742 time to fit residues: 89.0410 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17078 Z= 0.183 Angle : 0.596 7.279 25918 Z= 0.310 Chirality : 0.032 0.227 3318 Planarity : 0.006 0.136 1121 Dihedral : 25.364 179.596 9130 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 5.57 % Allowed : 33.43 % 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: 0.95 (0.41), residues: 381 helix: 1.19 (0.31), residues: 260 sheet: 0.86 (0.97), residues: 24 loop : -0.83 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 357 HIS 0.002 0.001 HIS D 109 PHE 0.011 0.002 PHE D 298 TYR 0.020 0.002 TYR D 385 ARG 0.007 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: 19 poor density : 45 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 149 VAL cc_start: 0.7058 (OUTLIER) cc_final: 0.6764 (p) REVERT: D 270 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7586 (tp) REVERT: D 300 LYS cc_start: 0.8240 (tttm) cc_final: 0.7920 (mmmt) outliers start: 19 outliers final: 8 residues processed: 61 average time/residue: 1.2692 time to fit residues: 86.0474 Evaluate side-chains 48 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7952 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17078 Z= 0.231 Angle : 0.633 7.829 25918 Z= 0.330 Chirality : 0.035 0.262 3318 Planarity : 0.006 0.131 1121 Dihedral : 25.353 177.952 9130 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 6.74 % Allowed : 32.84 % 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: 0.76 (0.41), residues: 381 helix: 1.03 (0.30), residues: 260 sheet: 0.88 (0.95), residues: 24 loop : -0.90 (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 0.013 0.002 PHE D 298 TYR 0.026 0.002 TYR D 385 ARG 0.003 0.000 ARG D 217 *********************** 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 64 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 41 time to evaluate : 0.710 Fit side-chains REVERT: D 146 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6235 (t80) REVERT: D 149 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6918 (p) REVERT: D 214 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6575 (mmt) REVERT: D 270 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7579 (tp) REVERT: D 300 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7957 (mmmt) REVERT: D 347 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6564 (mmp80) REVERT: D 358 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.7712 (tttm) outliers start: 23 outliers final: 9 residues processed: 59 average time/residue: 1.2548 time to fit residues: 82.8922 Evaluate side-chains 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 386 THR 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: 3.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN D 128 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3033 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= 0.292 Angle : 0.692 9.941 25918 Z= 0.358 Chirality : 0.038 0.248 3318 Planarity : 0.006 0.126 1121 Dihedral : 25.421 177.248 9130 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 6.45 % Allowed : 32.55 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.41), residues: 381 helix: 0.85 (0.30), residues: 256 sheet: 0.79 (0.98), residues: 24 loop : -1.12 (0.61), residues: 101 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 0.013 0.002 PHE D 298 TYR 0.027 0.002 TYR D 385 ARG 0.003 0.001 ARG D 25 *********************** 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 61 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 39 time to evaluate : 0.950 Fit side-chains REVERT: D 146 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6423 (t80) REVERT: D 149 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6988 (p) REVERT: D 214 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6469 (mmt) REVERT: D 270 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7620 (tp) REVERT: D 300 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (mmmt) REVERT: D 347 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6621 (mmp80) outliers start: 22 outliers final: 9 residues processed: 54 average time/residue: 1.1393 time to fit residues: 69.1234 Evaluate side-chains 51 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 386 THR 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: 0.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 56 optimal weight: 0.1980 chunk 36 optimal weight: 5.9990 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 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3031 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= 0.221 Angle : 0.646 9.773 25918 Z= 0.338 Chirality : 0.035 0.244 3318 Planarity : 0.006 0.123 1121 Dihedral : 25.404 177.677 9130 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.67 % Favored : 95.80 % Rotamer: Outliers : 6.16 % Allowed : 32.84 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.41), residues: 381 helix: 0.91 (0.31), residues: 256 sheet: 0.52 (1.00), residues: 24 loop : -1.12 (0.61), residues: 101 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 0.014 0.002 PHE D 298 TYR 0.024 0.002 TYR D 385 ARG 0.003 0.000 ARG D 172 *********************** 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 58 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 37 time to evaluate : 0.757 Fit side-chains REVERT: D 141 ASP cc_start: 0.5595 (t0) cc_final: 0.5370 (t0) REVERT: D 146 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6366 (t80) REVERT: D 149 VAL cc_start: 0.7229 (OUTLIER) cc_final: 0.6966 (p) REVERT: D 270 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7631 (tp) REVERT: D 300 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7951 (mmmt) REVERT: D 347 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6541 (mmp80) REVERT: D 358 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.7769 (tttm) outliers start: 21 outliers final: 9 residues processed: 52 average time/residue: 1.2169 time to fit residues: 70.5947 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 10.0000 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: 0.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.0470 chunk 80 optimal weight: 0.8980 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7927 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17078 Z= 0.178 Angle : 0.615 11.002 25918 Z= 0.320 Chirality : 0.033 0.228 3318 Planarity : 0.006 0.122 1121 Dihedral : 25.336 178.808 9130 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.99 % Allowed : 33.43 % Favored : 61.58 % 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: 0.77 (0.42), residues: 381 helix: 1.17 (0.31), residues: 256 sheet: 0.21 (1.01), residues: 24 loop : -1.01 (0.62), residues: 101 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 0.010 0.002 PHE D 298 TYR 0.019 0.002 TYR D 385 ARG 0.003 0.000 ARG D 172 *********************** 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 56 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.788 Fit side-chains REVERT: D 146 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6398 (t80) REVERT: D 149 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6977 (p) REVERT: D 214 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6495 (mmt) REVERT: D 270 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7569 (tp) REVERT: D 300 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7925 (mmmt) REVERT: D 347 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6505 (mmp80) REVERT: D 358 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7732 (tttm) outliers start: 17 outliers final: 6 residues processed: 51 average time/residue: 1.2231 time to fit residues: 69.8637 Evaluate side-chains 50 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.0060 chunk 51 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17078 Z= 0.183 Angle : 0.600 10.759 25918 Z= 0.313 Chirality : 0.033 0.223 3318 Planarity : 0.006 0.121 1121 Dihedral : 25.252 179.258 9130 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.41 % Favored : 96.06 % Rotamer: Outliers : 4.99 % Allowed : 33.14 % Favored : 61.88 % 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: 0.91 (0.42), residues: 381 helix: 1.29 (0.31), residues: 259 sheet: 0.06 (0.97), residues: 24 loop : -1.01 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.002 0.001 HIS D 109 PHE 0.011 0.002 PHE D 298 TYR 0.021 0.001 TYR D 385 ARG 0.002 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 58 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.759 Fit side-chains REVERT: D 146 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6359 (t80) REVERT: D 149 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6976 (p) REVERT: D 214 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6511 (mmt) REVERT: D 270 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7619 (tp) REVERT: D 300 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7945 (mmmt) REVERT: D 347 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6494 (mmp80) REVERT: D 358 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7737 (tttm) outliers start: 17 outliers final: 8 residues processed: 52 average time/residue: 1.3196 time to fit residues: 76.0304 Evaluate side-chains 53 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS 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: 2.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 ASN D 258 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17078 Z= 0.249 Angle : 0.642 10.446 25918 Z= 0.333 Chirality : 0.035 0.230 3318 Planarity : 0.006 0.119 1121 Dihedral : 25.262 177.891 9130 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % 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: 0.60 (0.42), residues: 381 helix: 1.06 (0.31), residues: 255 sheet: 0.16 (1.00), residues: 24 loop : -1.12 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.004 0.001 HIS D 284 PHE 0.015 0.002 PHE D 298 TYR 0.027 0.002 TYR D 385 ARG 0.002 0.000 ARG D 88 ********************** 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 54 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 0.779 Fit side-chains REVERT: D 146 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6440 (t80) REVERT: D 149 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.7008 (p) REVERT: D 214 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6502 (mmt) REVERT: D 231 MET cc_start: 0.7191 (mpp) cc_final: 0.6921 (mpp) REVERT: D 270 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7608 (tp) REVERT: D 300 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7974 (mmmt) REVERT: D 347 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6619 (mmp80) REVERT: D 358 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.7775 (tttm) outliers start: 17 outliers final: 9 residues processed: 49 average time/residue: 1.2528 time to fit residues: 68.4336 Evaluate side-chains 52 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.0000 chunk 4 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 128 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 = 0.4335 r_free = 0.4335 target = 0.196911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.153633 restraints weight = 20008.464| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 0.93 r_work: 0.3518 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17078 Z= 0.303 Angle : 0.690 10.684 25918 Z= 0.358 Chirality : 0.038 0.261 3318 Planarity : 0.006 0.118 1121 Dihedral : 25.350 177.660 9130 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.94 % Favored : 95.54 % Rotamer: Outliers : 5.28 % Allowed : 34.31 % 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: 0.37 (0.42), residues: 381 helix: 0.88 (0.31), residues: 255 sheet: 0.54 (1.04), residues: 24 loop : -1.33 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.005 0.002 HIS D 109 PHE 0.017 0.003 PHE D 298 TYR 0.027 0.002 TYR D 385 ARG 0.004 0.001 ARG D 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.98 seconds wall clock time: 60 minutes 3.78 seconds (3603.78 seconds total)