Starting phenix.real_space_refine on Wed Mar 12 15:40:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8squ_40713/03_2025/8squ_40713_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8squ_40713/03_2025/8squ_40713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8squ_40713/03_2025/8squ_40713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8squ_40713/03_2025/8squ_40713.map" model { file = "/net/cci-nas-00/data/ceres_data/8squ_40713/03_2025/8squ_40713_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8squ_40713/03_2025/8squ_40713_neut.cif" } resolution = 3.28 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= -0.002 sd= 0.030 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 41 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4876 2.51 5 N 1295 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7761 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3120 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 360} Chain breaks: 4 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.68 Number of scatterers: 7761 At special positions: 0 Unit cell: (81.7, 104.5, 120.65, 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 22 16.00 P 41 15.00 Mg 1 11.99 O 1526 8.00 N 1295 7.00 C 4876 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: 2.29 Conformation dependent library (CDL) restraints added in 821.2 milliseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 36.5% alpha, 15.7% beta 9 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.101A pdb=" N GLY A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.781A pdb=" N LYS A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.872A pdb=" N ILE A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.672A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.516A pdb=" N PHE B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.794A pdb=" N GLN B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.702A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 3.615A pdb=" N ARG B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.734A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 4.082A pdb=" N GLN B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 366 through 376 removed outlier: 4.034A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 480 Processing helix chain 'B' and resid 481 through 490 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.542A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 286 removed outlier: 6.542A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 176 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TRP A 175 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU A 406 " --> pdb=" O TRP A 175 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 401 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 403 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.598A pdb=" N VAL B 413 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.503A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.835A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.705A pdb=" N GLN B 302 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 314 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 304 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 267 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.67 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: 1819 1.33 - 1.45: 1869 1.45 - 1.57: 4234 1.57 - 1.69: 80 1.69 - 1.81: 33 Bond restraints: 8035 Sorted by residual: bond pdb=" O5' G C 20 " pdb=" C5' G C 20 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.72e+00 bond pdb=" O5' U C 21 " pdb=" C5' U C 21 " ideal model delta sigma weight residual 1.424 1.452 -0.028 1.50e-02 4.44e+03 3.50e+00 bond pdb=" O5' U C 10 " pdb=" C5' U C 10 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.85e+00 bond pdb=" O5' U C 13 " pdb=" C5' U C 13 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.76e+00 bond pdb=" P G C 20 " pdb=" OP2 G C 20 " ideal model delta sigma weight residual 1.485 1.518 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 8030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10815 2.00 - 4.00: 179 4.00 - 5.99: 33 5.99 - 7.99: 5 7.99 - 9.99: 1 Bond angle restraints: 11033 Sorted by residual: angle pdb=" CA MET B 303 " pdb=" CB MET B 303 " pdb=" CG MET B 303 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA ARG A 197 " pdb=" CB ARG A 197 " pdb=" CG ARG A 197 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" N GLU B 476 " pdb=" CA GLU B 476 " pdb=" C GLU B 476 " ideal model delta sigma weight residual 109.48 103.90 5.58 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C3' A C 12 " pdb=" C2' A C 12 " pdb=" C1' A C 12 " ideal model delta sigma weight residual 101.30 104.36 -3.06 1.00e+00 1.00e+00 9.38e+00 angle pdb=" O5' U C 13 " pdb=" C5' U C 13 " pdb=" C4' U C 13 " ideal model delta sigma weight residual 111.50 106.95 4.55 1.50e+00 4.44e-01 9.20e+00 ... (remaining 11028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 4599 35.51 - 71.02: 160 71.02 - 106.53: 11 106.53 - 142.04: 2 142.04 - 177.55: 4 Dihedral angle restraints: 4776 sinusoidal: 2304 harmonic: 2472 Sorted by residual: dihedral pdb=" O4' U C 17 " pdb=" C1' U C 17 " pdb=" N1 U C 17 " pdb=" C2 U C 17 " ideal model delta sinusoidal sigma weight residual 200.00 45.61 154.39 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U C 13 " pdb=" C1' U C 13 " pdb=" N1 U C 13 " pdb=" C2 U C 13 " ideal model delta sinusoidal sigma weight residual 200.00 74.41 125.59 1 1.50e+01 4.44e-03 6.75e+01 dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -128.00 49.55 -177.55 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 4773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1157 0.105 - 0.210: 43 0.210 - 0.315: 0 0.315 - 0.419: 3 0.419 - 0.524: 3 Chirality restraints: 1206 Sorted by residual: chirality pdb=" P U C 10 " pdb=" OP1 U C 10 " pdb=" OP2 U C 10 " pdb=" O5' U C 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" P U C 21 " pdb=" OP1 U C 21 " pdb=" OP2 U C 21 " pdb=" O5' U C 21 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" P G C 20 " pdb=" OP1 G C 20 " pdb=" OP2 G C 20 " pdb=" O5' G C 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 1203 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 331 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 332 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 332 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 332 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 430 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C GLN B 430 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN B 430 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 431 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 181 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 182 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.021 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 53 2.55 - 3.14: 5763 3.14 - 3.73: 12155 3.73 - 4.31: 16269 4.31 - 4.90: 25918 Nonbonded interactions: 60158 Sorted by model distance: nonbonded pdb=" O TYR B 506 " pdb="MG MG B 601 " model vdw 1.967 2.170 nonbonded pdb=" OP2 U C 1 " pdb="MG MG B 601 " model vdw 1.976 2.170 nonbonded pdb=" OP1 U C 1 " pdb="MG MG B 601 " model vdw 2.087 2.170 nonbonded pdb=" O GLY B 487 " pdb=" OG1 THR B 491 " model vdw 2.117 3.040 nonbonded pdb=" OG SER B 291 " pdb=" O ASN B 293 " model vdw 2.167 3.040 ... (remaining 60153 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 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 : 0.003 0.046 8035 Z= 0.199 Angle : 0.625 9.991 11033 Z= 0.326 Chirality : 0.054 0.524 1206 Planarity : 0.004 0.057 1244 Dihedral : 18.098 177.551 3178 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.30), residues: 827 helix: 1.71 (0.33), residues: 275 sheet: -0.53 (0.47), residues: 138 loop : -1.89 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.002 0.001 HIS B 329 PHE 0.020 0.002 PHE B 373 TYR 0.011 0.001 TYR A 293 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8279 (m-30) cc_final: 0.7875 (m-30) REVERT: B 303 MET cc_start: 0.4240 (mmp) cc_final: 0.2824 (tpt) REVERT: B 396 LEU cc_start: 0.6911 (mt) cc_final: 0.6116 (mt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2234 time to fit residues: 53.3477 Evaluate side-chains 90 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.0470 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN B 61 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.152429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.120422 restraints weight = 20222.509| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 6.05 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8035 Z= 0.213 Angle : 0.669 8.903 11033 Z= 0.344 Chirality : 0.046 0.372 1206 Planarity : 0.004 0.053 1244 Dihedral : 19.116 177.337 1453 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.93 % Allowed : 11.58 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.29), residues: 827 helix: 1.69 (0.32), residues: 283 sheet: -0.55 (0.45), residues: 150 loop : -1.81 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 319 HIS 0.003 0.001 HIS B 329 PHE 0.014 0.002 PHE B 82 TYR 0.021 0.001 TYR A 416 ARG 0.004 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8823 (mp0) cc_final: 0.8353 (pm20) REVERT: A 210 TYR cc_start: 0.7988 (t80) cc_final: 0.7701 (t80) REVERT: A 273 PHE cc_start: 0.7236 (t80) cc_final: 0.6808 (t80) REVERT: A 277 MET cc_start: 0.8878 (mmp) cc_final: 0.8603 (mmp) REVERT: A 339 SER cc_start: 0.8549 (m) cc_final: 0.8147 (t) REVERT: B 82 PHE cc_start: 0.7433 (m-80) cc_final: 0.7114 (m-80) REVERT: B 83 ASP cc_start: 0.8040 (t0) cc_final: 0.7705 (t0) REVERT: B 145 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5416 (p0) REVERT: B 226 GLU cc_start: 0.7678 (tt0) cc_final: 0.7052 (mt-10) REVERT: B 396 LEU cc_start: 0.6828 (mt) cc_final: 0.6237 (mt) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.2077 time to fit residues: 30.8037 Evaluate side-chains 87 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 431 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.150743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.118714 restraints weight = 21208.108| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 6.05 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8035 Z= 0.201 Angle : 0.631 8.557 11033 Z= 0.325 Chirality : 0.044 0.313 1206 Planarity : 0.004 0.050 1244 Dihedral : 19.247 177.504 1453 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.60 % Allowed : 13.32 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 827 helix: 1.78 (0.32), residues: 283 sheet: -0.42 (0.46), residues: 148 loop : -1.80 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 370 HIS 0.008 0.001 HIS A 358 PHE 0.012 0.001 PHE A 332 TYR 0.011 0.001 TYR B 505 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8745 (mp0) cc_final: 0.8396 (pm20) REVERT: A 210 TYR cc_start: 0.7974 (t80) cc_final: 0.7707 (t80) REVERT: A 273 PHE cc_start: 0.7393 (t80) cc_final: 0.6906 (t80) REVERT: A 277 MET cc_start: 0.8947 (mmp) cc_final: 0.8665 (mmp) REVERT: A 339 SER cc_start: 0.8502 (m) cc_final: 0.8038 (t) REVERT: B 82 PHE cc_start: 0.7577 (m-80) cc_final: 0.7297 (m-80) REVERT: B 83 ASP cc_start: 0.8003 (t0) cc_final: 0.7693 (t0) REVERT: B 226 GLU cc_start: 0.7751 (tt0) cc_final: 0.7171 (mt-10) REVERT: B 303 MET cc_start: 0.4942 (mmm) cc_final: 0.4662 (mmm) REVERT: B 399 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6795 (p) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 0.1791 time to fit residues: 25.7724 Evaluate side-chains 95 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 507 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.112261 restraints weight = 21497.811| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 6.27 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8035 Z= 0.299 Angle : 0.689 8.043 11033 Z= 0.359 Chirality : 0.046 0.243 1206 Planarity : 0.004 0.052 1244 Dihedral : 19.441 177.848 1453 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.66 % Allowed : 13.18 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.54 (0.29), residues: 827 helix: 1.60 (0.31), residues: 285 sheet: -0.69 (0.46), residues: 146 loop : -1.76 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 319 HIS 0.005 0.001 HIS A 358 PHE 0.021 0.002 PHE A 223 TYR 0.015 0.002 TYR A 416 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.8261 (p0) cc_final: 0.7993 (p0) REVERT: A 210 TYR cc_start: 0.7982 (t80) cc_final: 0.6924 (t80) REVERT: A 318 ASN cc_start: 0.8375 (m-40) cc_final: 0.8168 (m-40) REVERT: A 339 SER cc_start: 0.8651 (m) cc_final: 0.8129 (t) REVERT: A 387 ASP cc_start: 0.5272 (OUTLIER) cc_final: 0.4999 (p0) REVERT: A 395 MET cc_start: 0.7578 (mtt) cc_final: 0.7259 (mtt) REVERT: A 411 LYS cc_start: 0.8394 (tmtt) cc_final: 0.8125 (tmmt) REVERT: B 36 LEU cc_start: 0.7572 (mm) cc_final: 0.7297 (mm) REVERT: B 83 ASP cc_start: 0.7994 (t0) cc_final: 0.7693 (t0) REVERT: B 303 MET cc_start: 0.6201 (mmm) cc_final: 0.5709 (mmp) REVERT: B 399 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7077 (p) outliers start: 20 outliers final: 11 residues processed: 98 average time/residue: 0.2054 time to fit residues: 28.5230 Evaluate side-chains 86 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.108403 restraints weight = 22248.585| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 6.17 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8035 Z= 0.377 Angle : 0.751 10.635 11033 Z= 0.392 Chirality : 0.048 0.290 1206 Planarity : 0.005 0.064 1244 Dihedral : 19.725 179.633 1453 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.20 % Allowed : 15.45 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.29), residues: 827 helix: 1.36 (0.32), residues: 285 sheet: -0.92 (0.44), residues: 150 loop : -1.87 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 86 HIS 0.015 0.002 HIS A 358 PHE 0.027 0.003 PHE A 223 TYR 0.026 0.002 TYR A 171 ARG 0.004 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8269 (mtm) cc_final: 0.7964 (ptm) REVERT: A 339 SER cc_start: 0.8673 (m) cc_final: 0.8119 (t) REVERT: A 395 MET cc_start: 0.7556 (mtt) cc_final: 0.7341 (mtt) REVERT: B 36 LEU cc_start: 0.7260 (mm) cc_final: 0.7047 (mm) outliers start: 24 outliers final: 17 residues processed: 91 average time/residue: 0.1692 time to fit residues: 22.1284 Evaluate side-chains 86 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 75 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.147766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.115332 restraints weight = 21275.822| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 6.26 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8035 Z= 0.183 Angle : 0.653 10.025 11033 Z= 0.335 Chirality : 0.044 0.234 1206 Planarity : 0.004 0.061 1244 Dihedral : 19.787 179.269 1453 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.60 % Allowed : 17.18 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.29), residues: 827 helix: 1.72 (0.31), residues: 285 sheet: -0.81 (0.45), residues: 141 loop : -1.71 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 319 HIS 0.008 0.001 HIS A 358 PHE 0.012 0.001 PHE A 321 TYR 0.011 0.001 TYR B 505 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8796 (tt) REVERT: A 273 PHE cc_start: 0.7263 (t80) cc_final: 0.6954 (t80) REVERT: A 287 MET cc_start: 0.8314 (mtm) cc_final: 0.8060 (ptm) REVERT: B 36 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6936 (mm) REVERT: B 83 ASP cc_start: 0.7863 (t0) cc_final: 0.7603 (t0) REVERT: B 279 CYS cc_start: 0.8170 (p) cc_final: 0.7901 (p) REVERT: B 303 MET cc_start: 0.5556 (mmm) cc_final: 0.4030 (mpp) REVERT: B 399 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6620 (p) outliers start: 12 outliers final: 5 residues processed: 91 average time/residue: 0.1865 time to fit residues: 24.1757 Evaluate side-chains 86 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.146345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.113511 restraints weight = 21741.066| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 6.50 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8035 Z= 0.211 Angle : 0.650 11.129 11033 Z= 0.336 Chirality : 0.044 0.249 1206 Planarity : 0.004 0.061 1244 Dihedral : 19.857 178.307 1453 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.86 % Allowed : 18.11 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 827 helix: 1.81 (0.32), residues: 285 sheet: -0.78 (0.44), residues: 151 loop : -1.67 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 319 HIS 0.011 0.001 HIS A 358 PHE 0.011 0.001 PHE B 419 TYR 0.021 0.001 TYR A 416 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7661 (t80) cc_final: 0.7016 (t80) REVERT: A 273 PHE cc_start: 0.7310 (t80) cc_final: 0.7099 (t80) REVERT: A 287 MET cc_start: 0.8404 (mtm) cc_final: 0.7998 (ptm) REVERT: A 328 LYS cc_start: 0.8350 (mttm) cc_final: 0.8108 (mttm) REVERT: A 395 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7230 (mtp) REVERT: B 36 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6623 (mm) REVERT: B 83 ASP cc_start: 0.7976 (t0) cc_final: 0.7715 (t0) REVERT: B 279 CYS cc_start: 0.7978 (p) cc_final: 0.7724 (p) REVERT: B 399 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6703 (p) outliers start: 14 outliers final: 7 residues processed: 85 average time/residue: 0.1719 time to fit residues: 20.9517 Evaluate side-chains 88 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.147243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.115074 restraints weight = 21748.954| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 6.45 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8035 Z= 0.196 Angle : 0.653 12.940 11033 Z= 0.333 Chirality : 0.044 0.249 1206 Planarity : 0.004 0.061 1244 Dihedral : 19.888 177.484 1453 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.86 % Allowed : 18.64 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.30), residues: 827 helix: 1.83 (0.32), residues: 287 sheet: -0.82 (0.43), residues: 151 loop : -1.62 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 319 HIS 0.009 0.001 HIS A 358 PHE 0.013 0.001 PHE B 304 TYR 0.020 0.001 TYR A 416 ARG 0.002 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.7413 (OUTLIER) cc_final: 0.7102 (p) REVERT: A 395 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7126 (mtp) REVERT: A 411 LYS cc_start: 0.8363 (tmtt) cc_final: 0.8120 (tttm) REVERT: B 36 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6533 (mm) REVERT: B 83 ASP cc_start: 0.7995 (t0) cc_final: 0.7739 (t0) REVERT: B 279 CYS cc_start: 0.8031 (p) cc_final: 0.7765 (p) REVERT: B 303 MET cc_start: 0.5285 (mmm) cc_final: 0.3440 (mmt) REVERT: B 399 THR cc_start: 0.7067 (OUTLIER) cc_final: 0.6626 (p) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 0.1914 time to fit residues: 25.1227 Evaluate side-chains 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.144692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.111145 restraints weight = 22360.930| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 6.74 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8035 Z= 0.258 Angle : 0.696 15.813 11033 Z= 0.357 Chirality : 0.045 0.268 1206 Planarity : 0.004 0.064 1244 Dihedral : 19.914 177.685 1453 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.13 % Allowed : 18.38 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.42 (0.30), residues: 827 helix: 1.75 (0.32), residues: 288 sheet: -0.93 (0.45), residues: 135 loop : -1.61 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 319 HIS 0.009 0.001 HIS A 358 PHE 0.016 0.002 PHE A 223 TYR 0.018 0.002 TYR A 416 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 324 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.6975 (p) REVERT: A 339 SER cc_start: 0.8528 (m) cc_final: 0.7979 (t) REVERT: A 395 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: A 411 LYS cc_start: 0.8471 (tmtt) cc_final: 0.8175 (tttm) REVERT: B 36 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6770 (mm) REVERT: B 83 ASP cc_start: 0.8336 (t0) cc_final: 0.8049 (t0) REVERT: B 303 MET cc_start: 0.5632 (mmm) cc_final: 0.4114 (mpp) REVERT: B 399 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6796 (p) REVERT: B 453 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.6115 (mmmt) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.1721 time to fit residues: 22.4044 Evaluate side-chains 94 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 chunk 62 optimal weight: 8.9990 chunk 3 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 overall best weight: 0.8416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.147936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.114402 restraints weight = 21970.998| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 6.70 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8035 Z= 0.191 Angle : 0.676 16.626 11033 Z= 0.344 Chirality : 0.044 0.251 1206 Planarity : 0.004 0.062 1244 Dihedral : 19.954 177.846 1453 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.73 % Allowed : 19.04 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.36 (0.29), residues: 827 helix: 1.75 (0.32), residues: 287 sheet: -0.80 (0.45), residues: 134 loop : -1.57 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 319 HIS 0.008 0.001 HIS A 358 PHE 0.021 0.002 PHE A 198 TYR 0.023 0.001 TYR A 210 ARG 0.003 0.000 ARG B 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 339 SER cc_start: 0.8523 (m) cc_final: 0.7983 (t) REVERT: A 395 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6982 (mtp) REVERT: A 411 LYS cc_start: 0.8455 (tmtt) cc_final: 0.8178 (tttm) REVERT: B 36 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6639 (mm) REVERT: B 83 ASP cc_start: 0.8350 (t0) cc_final: 0.8075 (t0) REVERT: B 303 MET cc_start: 0.5621 (mmm) cc_final: 0.4074 (mpp) REVERT: B 399 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6523 (p) REVERT: B 453 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5930 (mmmt) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 0.1919 time to fit residues: 24.7789 Evaluate side-chains 88 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 79 optimal weight: 0.0020 chunk 19 optimal weight: 4.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.148382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.114748 restraints weight = 21977.714| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 6.70 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8035 Z= 0.190 Angle : 0.681 16.813 11033 Z= 0.348 Chirality : 0.043 0.254 1206 Planarity : 0.004 0.059 1244 Dihedral : 19.975 179.411 1453 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.60 % Allowed : 19.57 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.36 (0.29), residues: 827 helix: 1.74 (0.32), residues: 288 sheet: -0.78 (0.45), residues: 134 loop : -1.57 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 319 HIS 0.008 0.001 HIS A 358 PHE 0.023 0.002 PHE A 273 TYR 0.024 0.001 TYR A 210 ARG 0.003 0.000 ARG B 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4128.09 seconds wall clock time: 72 minutes 56.69 seconds (4376.69 seconds total)