Starting phenix.real_space_refine on Wed Feb 12 16:48:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utn_26782/02_2025/7utn_26782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utn_26782/02_2025/7utn_26782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7utn_26782/02_2025/7utn_26782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utn_26782/02_2025/7utn_26782.map" model { file = "/net/cci-nas-00/data/ceres_data/7utn_26782/02_2025/7utn_26782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utn_26782/02_2025/7utn_26782.cif" } resolution = 2.74 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= -0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 228 5.49 5 S 21 5.16 5 C 4183 2.51 5 N 1470 2.21 5 O 2101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3174 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 90, 'rna3p_pyr': 68} Link IDs: {'rna2p': 25, 'rna3p': 158} Chain breaks: 2 Chain: "A" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 579 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Time building chain proxies: 5.61, per 1000 atoms: 0.70 Number of scatterers: 8003 At special positions: 0 Unit cell: (90.95, 105.93, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 228 15.00 O 2101 8.00 N 1470 7.00 C 4183 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 - 3.00 Amino acid : True - 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: 2.25 Conformation dependent library (CDL) restraints added in 436.2 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 30.0% alpha, 20.4% beta 76 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 88 through 109 removed outlier: 4.313A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.662A pdb=" N ILE D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 314 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.588A pdb=" N TYR D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 6.264A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.231A pdb=" N VAL D 189 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 321 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 191 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 57 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU D 192 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE D 59 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 79 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 369 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N MET D 366 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 380 removed outlier: 6.559A pdb=" N GLN D 432 " --> pdb=" O HIS D 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 392 through 395 removed outlier: 6.610A pdb=" N TYR D 387 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 476 through 478 removed outlier: 4.836A pdb=" N VAL D 466 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY D 460 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR D 468 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER D 458 " --> pdb=" O TYR D 468 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 470 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 444 " --> pdb=" O LEU D 485 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 364 hydrogen bond angles 0 basepair planarities 76 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1144 1.33 - 1.45: 3372 1.45 - 1.56: 3635 1.56 - 1.68: 451 1.68 - 1.80: 33 Bond restraints: 8635 Sorted by residual: bond pdb=" O3' U C 205 " pdb=" P U C 206 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.50e+00 bond pdb=" N ASN D 65 " pdb=" CA ASN D 65 " ideal model delta sigma weight residual 1.466 1.443 0.023 1.36e-02 5.41e+03 2.93e+00 bond pdb=" CA ARG D 151 " pdb=" CB ARG D 151 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.75e-02 3.27e+03 2.93e+00 bond pdb=" SD MET D 68 " pdb=" CE MET D 68 " ideal model delta sigma weight residual 1.791 1.748 0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" N ARG D 330 " pdb=" CA ARG D 330 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.17e-02 7.31e+03 2.43e+00 ... (remaining 8630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 12339 1.72 - 3.43: 338 3.43 - 5.15: 54 5.15 - 6.87: 4 6.87 - 8.58: 1 Bond angle restraints: 12736 Sorted by residual: angle pdb=" C4' U C 206 " pdb=" C3' U C 206 " pdb=" O3' U C 206 " ideal model delta sigma weight residual 109.40 117.98 -8.58 1.50e+00 4.44e-01 3.27e+01 angle pdb=" C3' A C 128 " pdb=" C2' A C 128 " pdb=" C1' A C 128 " ideal model delta sigma weight residual 101.50 105.10 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" C4' A C 128 " pdb=" C3' A C 128 " pdb=" O3' A C 128 " ideal model delta sigma weight residual 109.40 114.76 -5.36 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C3' A C 78 " pdb=" C2' A C 78 " pdb=" C1' A C 78 " ideal model delta sigma weight residual 101.30 104.71 -3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" C2' A C 78 " pdb=" C1' A C 78 " pdb=" N9 A C 78 " ideal model delta sigma weight residual 112.00 106.96 5.04 1.50e+00 4.44e-01 1.13e+01 ... (remaining 12731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 4683 35.57 - 71.15: 533 71.15 - 106.72: 52 106.72 - 142.29: 4 142.29 - 177.87: 10 Dihedral angle restraints: 5282 sinusoidal: 4127 harmonic: 1155 Sorted by residual: dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 36.86 163.14 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U C 204 " pdb=" C1' U C 204 " pdb=" N1 U C 204 " pdb=" C2 U C 204 " ideal model delta sinusoidal sigma weight residual 200.00 46.30 153.70 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U C 180 " pdb=" C1' U C 180 " pdb=" N1 U C 180 " pdb=" C2 U C 180 " ideal model delta sinusoidal sigma weight residual -160.00 -28.49 -131.51 1 1.50e+01 4.44e-03 7.09e+01 ... (remaining 5279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1455 0.072 - 0.144: 101 0.144 - 0.216: 7 0.216 - 0.288: 3 0.288 - 0.361: 1 Chirality restraints: 1567 Sorted by residual: chirality pdb=" C3' A C 128 " pdb=" C4' A C 128 " pdb=" O3' A C 128 " pdb=" C2' A C 128 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C2' A C 78 " pdb=" C3' A C 78 " pdb=" O2' A C 78 " pdb=" C1' A C 78 " both_signs ideal model delta sigma weight residual False -2.75 -2.48 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1' G C 121 " pdb=" O4' G C 121 " pdb=" C2' G C 121 " pdb=" N9 G C 121 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1564 not shown) Planarity restraints: 787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 78 " -0.042 2.00e-02 2.50e+03 2.12e-02 1.24e+01 pdb=" N9 A C 78 " 0.055 2.00e-02 2.50e+03 pdb=" C8 A C 78 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 78 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 78 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A C 78 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A C 78 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A C 78 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 78 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 78 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A C 78 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 91 " -0.034 2.00e-02 2.50e+03 1.45e-02 6.27e+00 pdb=" N9 G C 91 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G C 91 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G C 91 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 91 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G C 91 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 163 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 164 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.031 5.00e-02 4.00e+02 ... (remaining 784 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 226 2.64 - 3.21: 6504 3.21 - 3.77: 15156 3.77 - 4.34: 20706 4.34 - 4.90: 28300 Nonbonded interactions: 70892 Sorted by model distance: nonbonded pdb=" O2' A C 78 " pdb=" O4' G C 79 " model vdw 2.080 3.040 nonbonded pdb=" O4 U C 30 " pdb=" N6 A C 46 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG D 115 " pdb=" OP2 C C 58 " model vdw 2.223 3.120 nonbonded pdb=" OH TYR D 46 " pdb=" OP1 U C 206 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN D 487 " pdb=" N ASN D 488 " model vdw 2.321 3.120 ... (remaining 70887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.850 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: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.007 0.043 8635 Z= 0.407 Angle : 0.679 8.584 12736 Z= 0.394 Chirality : 0.041 0.361 1567 Planarity : 0.004 0.056 787 Dihedral : 23.532 177.868 4538 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.01 (0.40), residues: 393 helix: 1.09 (0.47), residues: 117 sheet: -0.44 (0.62), residues: 63 loop : -0.40 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 PHE 0.010 0.002 PHE D 453 TYR 0.010 0.001 TYR D 5 ARG 0.007 0.001 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.594 Fit side-chains REVERT: D 102 MET cc_start: 0.8634 (mmt) cc_final: 0.8320 (mmt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.7555 time to fit residues: 55.3507 Evaluate side-chains 22 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3301 r_free = 0.3301 target = 0.084178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.059187 restraints weight = 16689.001| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.44 r_work: 0.2691 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8635 Z= 0.244 Angle : 0.598 6.499 12736 Z= 0.325 Chirality : 0.037 0.301 1567 Planarity : 0.005 0.057 787 Dihedral : 24.387 176.893 3725 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.58 % Allowed : 4.36 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.40), residues: 393 helix: 1.71 (0.47), residues: 118 sheet: -0.12 (0.64), residues: 63 loop : -0.22 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 161 HIS 0.004 0.001 HIS D 104 PHE 0.007 0.001 PHE D 453 TYR 0.015 0.001 TYR D 327 ARG 0.004 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.517 Fit side-chains REVERT: D 102 MET cc_start: 0.9165 (mmt) cc_final: 0.8888 (mmt) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 1.6864 time to fit residues: 46.3769 Evaluate side-chains 23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3261 r_free = 0.3261 target = 0.082118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056931 restraints weight = 17025.389| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.50 r_work: 0.2636 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 8635 Z= 0.433 Angle : 0.665 6.918 12736 Z= 0.359 Chirality : 0.041 0.366 1567 Planarity : 0.005 0.062 787 Dihedral : 24.395 177.195 3725 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.87 % Allowed : 6.10 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.46 (0.40), residues: 393 helix: 1.69 (0.46), residues: 119 sheet: -0.01 (0.62), residues: 70 loop : -0.37 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 PHE 0.008 0.001 PHE D 453 TYR 0.022 0.002 TYR D 327 ARG 0.005 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.548 Fit side-chains REVERT: D 102 MET cc_start: 0.9171 (mmt) cc_final: 0.8891 (mmt) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 1.9452 time to fit residues: 50.9596 Evaluate side-chains 24 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3282 r_free = 0.3282 target = 0.083247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.058076 restraints weight = 16865.159| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.44 r_work: 0.2659 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8635 Z= 0.290 Angle : 0.614 6.709 12736 Z= 0.332 Chirality : 0.038 0.310 1567 Planarity : 0.005 0.058 787 Dihedral : 24.374 177.126 3725 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.87 % Allowed : 6.98 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.59 (0.41), residues: 393 helix: 1.86 (0.46), residues: 119 sheet: 0.01 (0.63), residues: 70 loop : -0.30 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 PHE 0.008 0.001 PHE D 453 TYR 0.009 0.001 TYR D 5 ARG 0.006 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.519 Fit side-chains REVERT: D 33 ARG cc_start: 0.7254 (ttp80) cc_final: 0.7023 (ttp80) REVERT: D 102 MET cc_start: 0.9194 (mmt) cc_final: 0.8926 (mmt) REVERT: D 355 LYS cc_start: 0.8716 (mmpt) cc_final: 0.8447 (mtmp) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 1.6273 time to fit residues: 43.0498 Evaluate side-chains 23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3275 r_free = 0.3275 target = 0.082895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057730 restraints weight = 16790.608| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.44 r_work: 0.2655 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8635 Z= 0.338 Angle : 0.623 6.613 12736 Z= 0.338 Chirality : 0.039 0.360 1567 Planarity : 0.005 0.059 787 Dihedral : 24.329 177.117 3725 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.16 % Allowed : 7.27 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.41), residues: 393 helix: 1.91 (0.46), residues: 119 sheet: -0.02 (0.63), residues: 70 loop : -0.21 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 161 HIS 0.003 0.001 HIS D 428 PHE 0.008 0.001 PHE D 453 TYR 0.009 0.001 TYR D 5 ARG 0.005 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.528 Fit side-chains REVERT: D 33 ARG cc_start: 0.7239 (ttp80) cc_final: 0.7021 (ttp80) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 1.7457 time to fit residues: 46.0095 Evaluate side-chains 23 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3308 r_free = 0.3308 target = 0.084677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.059609 restraints weight = 16727.262| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.46 r_work: 0.2697 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8635 Z= 0.207 Angle : 0.574 6.986 12736 Z= 0.310 Chirality : 0.035 0.291 1567 Planarity : 0.004 0.056 787 Dihedral : 24.304 177.048 3725 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.45 % Allowed : 7.27 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.41), residues: 393 helix: 2.10 (0.46), residues: 119 sheet: 0.06 (0.64), residues: 70 loop : -0.12 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 PHE 0.007 0.001 PHE D 453 TYR 0.009 0.001 TYR D 484 ARG 0.004 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.529 Fit side-chains REVERT: D 37 ARG cc_start: 0.8401 (ttp80) cc_final: 0.7824 (ttp-110) REVERT: D 73 GLU cc_start: 0.8133 (mp0) cc_final: 0.7853 (mp0) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 1.8428 time to fit residues: 54.3345 Evaluate side-chains 25 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3289 r_free = 0.3289 target = 0.083604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.058404 restraints weight = 16814.288| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.47 r_work: 0.2671 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8635 Z= 0.304 Angle : 0.599 6.707 12736 Z= 0.325 Chirality : 0.038 0.335 1567 Planarity : 0.004 0.057 787 Dihedral : 24.241 177.053 3725 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.87 % Allowed : 8.43 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.41), residues: 393 helix: 2.11 (0.47), residues: 119 sheet: 0.05 (0.64), residues: 70 loop : -0.12 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 161 HIS 0.002 0.001 HIS D 428 PHE 0.007 0.001 PHE D 453 TYR 0.012 0.001 TYR D 327 ARG 0.006 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.522 Fit side-chains REVERT: D 37 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7759 (ttp-110) REVERT: D 73 GLU cc_start: 0.8171 (mp0) cc_final: 0.7924 (mp0) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 1.8544 time to fit residues: 48.7793 Evaluate side-chains 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3314 r_free = 0.3314 target = 0.084980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.059833 restraints weight = 16899.127| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.47 r_work: 0.2705 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8635 Z= 0.187 Angle : 0.569 7.395 12736 Z= 0.307 Chirality : 0.035 0.311 1567 Planarity : 0.004 0.055 787 Dihedral : 24.252 176.996 3725 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.16 % Allowed : 7.56 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.42), residues: 393 helix: 2.19 (0.47), residues: 119 sheet: 0.13 (0.65), residues: 70 loop : -0.06 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 PHE 0.006 0.001 PHE D 453 TYR 0.009 0.001 TYR D 484 ARG 0.007 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.549 Fit side-chains REVERT: D 37 ARG cc_start: 0.8445 (ttp80) cc_final: 0.7890 (ttp-110) REVERT: D 392 LYS cc_start: 0.8599 (mptt) cc_final: 0.8387 (mmtp) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 1.7936 time to fit residues: 50.9060 Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3312 r_free = 0.3312 target = 0.084800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.059573 restraints weight = 17038.616| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.46 r_work: 0.2700 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8635 Z= 0.228 Angle : 0.571 6.592 12736 Z= 0.310 Chirality : 0.035 0.319 1567 Planarity : 0.004 0.055 787 Dihedral : 24.186 177.028 3725 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.87 % Allowed : 8.43 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 393 helix: 2.21 (0.46), residues: 121 sheet: 0.27 (0.71), residues: 61 loop : -0.21 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 PHE 0.007 0.001 PHE D 453 TYR 0.015 0.001 TYR D 327 ARG 0.007 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.538 Fit side-chains REVERT: D 37 ARG cc_start: 0.8424 (ttp80) cc_final: 0.7860 (ttp-110) REVERT: D 73 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8287 (mp0) REVERT: D 392 LYS cc_start: 0.8600 (mptt) cc_final: 0.8386 (mmtp) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 1.7865 time to fit residues: 50.8310 Evaluate side-chains 27 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 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 = 0.3267 r_free = 0.3267 target = 0.082458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.057167 restraints weight = 16841.623| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.51 r_work: 0.2645 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 8635 Z= 0.410 Angle : 0.646 7.003 12736 Z= 0.349 Chirality : 0.040 0.364 1567 Planarity : 0.005 0.056 787 Dihedral : 24.250 176.974 3725 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.58 % Allowed : 9.01 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.41), residues: 393 helix: 2.03 (0.47), residues: 119 sheet: -0.02 (0.65), residues: 70 loop : -0.15 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 428 PHE 0.008 0.001 PHE D 453 TYR 0.010 0.001 TYR D 5 ARG 0.006 0.001 ARG D 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: D 37 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7826 (ttp-110) REVERT: D 355 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8506 (mtmm) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 1.7979 time to fit residues: 45.3990 Evaluate side-chains 26 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 361 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** 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 = 0.3341 r_free = 0.3341 target = 0.086332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.061271 restraints weight = 16799.451| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.43 r_work: 0.2745 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8635 Z= 0.163 Angle : 0.549 7.295 12736 Z= 0.297 Chirality : 0.034 0.262 1567 Planarity : 0.004 0.056 787 Dihedral : 24.084 176.955 3725 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.87 % Allowed : 8.72 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.97 (0.42), residues: 393 helix: 2.24 (0.46), residues: 121 sheet: 0.19 (0.73), residues: 59 loop : -0.12 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.002 0.001 HIS D 104 PHE 0.007 0.001 PHE D 453 TYR 0.012 0.001 TYR D 327 ARG 0.007 0.000 ARG D 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5204.33 seconds wall clock time: 92 minutes 41.12 seconds (5561.12 seconds total)