Starting phenix.real_space_refine on Fri Aug 22 21:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8squ_40713/08_2025/8squ_40713_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8squ_40713/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2025/8squ_40713_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2025/8squ_40713_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2025/8squ_40713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2025/8squ_40713.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.29 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: 0.81 Conformation dependent library (CDL) restraints added in 412.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.02 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: 1.44 Time building geometry restraints manager: 1.07 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.660 Find NCS groups from input model: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- 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= 0.155 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 201 TYR 0.011 0.001 TYR A 293 PHE 0.020 0.002 PHE B 373 TRP 0.011 0.001 TRP B 370 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8035) covalent geometry : angle 0.62534 (11033) hydrogen bonds : bond 0.17918 ( 284) hydrogen bonds : angle 6.78074 ( 796) *********************** 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 : 0.301 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: 0.1041 time to fit residues: 25.0158 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 : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.4616 r_free = 0.4616 target = 0.153183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.121762 restraints weight = 20224.239| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 6.03 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2527 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= 0.140 Angle : 0.659 8.853 11033 Z= 0.339 Chirality : 0.046 0.350 1206 Planarity : 0.004 0.053 1244 Dihedral : 19.115 177.128 1453 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.80 % Allowed : 11.45 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.29), residues: 827 helix: 1.70 (0.32), residues: 283 sheet: -0.51 (0.44), residues: 150 loop : -1.80 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 374 TYR 0.021 0.001 TYR A 416 PHE 0.014 0.002 PHE A 198 TRP 0.014 0.001 TRP A 319 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8035) covalent geometry : angle 0.65898 (11033) hydrogen bonds : bond 0.03684 ( 284) hydrogen bonds : angle 4.76168 ( 796) *********************** 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 109 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8834 (mp0) cc_final: 0.8356 (pm20) REVERT: A 210 TYR cc_start: 0.7971 (t80) cc_final: 0.7692 (t80) REVERT: A 273 PHE cc_start: 0.7215 (t80) cc_final: 0.6790 (t80) REVERT: A 277 MET cc_start: 0.8880 (mmp) cc_final: 0.8604 (mmp) REVERT: A 395 MET cc_start: 0.7576 (mtt) cc_final: 0.7340 (mtp) REVERT: B 82 PHE cc_start: 0.7383 (m-80) cc_final: 0.7064 (m-80) REVERT: B 83 ASP cc_start: 0.8043 (t0) cc_final: 0.7718 (t0) REVERT: B 145 ASP cc_start: 0.5734 (OUTLIER) cc_final: 0.5527 (p0) REVERT: B 226 GLU cc_start: 0.7657 (tt0) cc_final: 0.7036 (mt-10) REVERT: B 396 LEU cc_start: 0.6845 (mt) cc_final: 0.6276 (mt) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.0871 time to fit residues: 12.8486 Evaluate side-chains 86 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 85 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.0060 chunk 57 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.4802 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.148850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.116726 restraints weight = 21075.719| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 6.03 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8035 Z= 0.163 Angle : 0.652 8.952 11033 Z= 0.337 Chirality : 0.045 0.318 1206 Planarity : 0.004 0.050 1244 Dihedral : 19.294 177.453 1453 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.86 % Allowed : 12.92 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.29), residues: 827 helix: 1.73 (0.32), residues: 284 sheet: -0.45 (0.45), residues: 147 loop : -1.82 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.010 0.001 TYR A 392 PHE 0.015 0.002 PHE A 332 TRP 0.012 0.001 TRP B 370 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8035) covalent geometry : angle 0.65230 (11033) hydrogen bonds : bond 0.03676 ( 284) hydrogen bonds : angle 4.47947 ( 796) *********************** 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 105 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8782 (mp0) cc_final: 0.8427 (pm20) REVERT: A 210 TYR cc_start: 0.8015 (t80) cc_final: 0.7748 (t80) REVERT: A 273 PHE cc_start: 0.7358 (t80) cc_final: 0.6851 (t80) REVERT: A 277 MET cc_start: 0.8950 (mmp) cc_final: 0.8640 (mmp) REVERT: A 395 MET cc_start: 0.7612 (mtt) cc_final: 0.7370 (mtp) REVERT: B 82 PHE cc_start: 0.7603 (m-80) cc_final: 0.7387 (m-80) REVERT: B 83 ASP cc_start: 0.7959 (t0) cc_final: 0.7644 (t0) REVERT: B 399 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6735 (p) outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 0.0887 time to fit residues: 12.4079 Evaluate side-chains 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 21 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.0980 chunk 76 optimal weight: 0.0060 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.151844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.119226 restraints weight = 21007.928| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 6.29 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3579 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= 0.125 Angle : 0.601 9.503 11033 Z= 0.310 Chirality : 0.043 0.226 1206 Planarity : 0.004 0.049 1244 Dihedral : 19.391 178.510 1453 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.86 % Allowed : 13.32 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.29), residues: 827 helix: 1.92 (0.32), residues: 284 sheet: -0.41 (0.45), residues: 148 loop : -1.77 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.014 0.001 TYR A 416 PHE 0.012 0.001 PHE A 380 TRP 0.017 0.001 TRP A 319 HIS 0.004 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8035) covalent geometry : angle 0.60113 (11033) hydrogen bonds : bond 0.03092 ( 284) hydrogen bonds : angle 4.19285 ( 796) *********************** 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 108 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8707 (mp0) cc_final: 0.8427 (pm20) REVERT: A 210 TYR cc_start: 0.7786 (t80) cc_final: 0.6997 (t80) REVERT: A 273 PHE cc_start: 0.7449 (t80) cc_final: 0.6935 (t80) REVERT: A 277 MET cc_start: 0.8989 (mmp) cc_final: 0.8775 (mmp) REVERT: A 395 MET cc_start: 0.7331 (mtt) cc_final: 0.7062 (mtp) REVERT: A 404 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 411 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7991 (tmmt) REVERT: B 36 LEU cc_start: 0.7409 (mm) cc_final: 0.7173 (mm) REVERT: B 82 PHE cc_start: 0.7334 (m-80) cc_final: 0.7023 (m-80) REVERT: B 83 ASP cc_start: 0.8041 (t0) cc_final: 0.7735 (t0) REVERT: B 226 GLU cc_start: 0.7722 (tt0) cc_final: 0.7119 (mt-10) REVERT: B 303 MET cc_start: 0.5470 (mmm) cc_final: 0.4766 (mmm) REVERT: B 407 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.5585 (ptp-110) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.0992 time to fit residues: 13.7031 Evaluate side-chains 89 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER 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 423 VAL Chi-restraints excluded: chain B residue 431 THR 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 28 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4633 r_free = 0.4633 target = 0.157228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.121334 restraints weight = 25018.168| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 7.14 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3899 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= 0.125 Angle : 0.609 11.508 11033 Z= 0.313 Chirality : 0.043 0.233 1206 Planarity : 0.004 0.052 1244 Dihedral : 19.453 177.906 1453 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.46 % Allowed : 14.78 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.30), residues: 827 helix: 2.00 (0.32), residues: 284 sheet: -0.46 (0.45), residues: 150 loop : -1.69 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.010 0.001 TYR B 411 PHE 0.011 0.001 PHE A 181 TRP 0.023 0.001 TRP A 319 HIS 0.006 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8035) covalent geometry : angle 0.60865 (11033) hydrogen bonds : bond 0.03131 ( 284) hydrogen bonds : angle 4.12552 ( 796) *********************** 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 97 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8819 (mp0) cc_final: 0.8556 (pm20) REVERT: A 210 TYR cc_start: 0.7962 (t80) cc_final: 0.7251 (t80) REVERT: A 273 PHE cc_start: 0.7405 (t80) cc_final: 0.6872 (t80) REVERT: A 277 MET cc_start: 0.8993 (mmp) cc_final: 0.8753 (mmp) REVERT: A 395 MET cc_start: 0.7186 (mtt) cc_final: 0.6927 (mtp) REVERT: A 404 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.9002 (p) REVERT: A 411 LYS cc_start: 0.8330 (tmtt) cc_final: 0.8036 (tmmt) REVERT: B 36 LEU cc_start: 0.7476 (mm) cc_final: 0.7203 (mm) REVERT: B 83 ASP cc_start: 0.8191 (t0) cc_final: 0.7876 (t0) REVERT: B 279 CYS cc_start: 0.8117 (p) cc_final: 0.7851 (p) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.0913 time to fit residues: 11.5990 Evaluate side-chains 88 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER 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 317 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.154124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.118075 restraints weight = 25090.004| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 7.20 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8035 Z= 0.154 Angle : 0.632 11.916 11033 Z= 0.326 Chirality : 0.043 0.242 1206 Planarity : 0.004 0.055 1244 Dihedral : 19.631 177.834 1453 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.86 % Allowed : 15.18 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.30), residues: 827 helix: 1.95 (0.32), residues: 285 sheet: -0.36 (0.46), residues: 144 loop : -1.74 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.016 0.001 TYR A 416 PHE 0.015 0.002 PHE B 304 TRP 0.027 0.001 TRP A 319 HIS 0.006 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8035) covalent geometry : angle 0.63207 (11033) hydrogen bonds : bond 0.03619 ( 284) hydrogen bonds : angle 4.19039 ( 796) *********************** 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 100 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8763 (tt) REVERT: A 273 PHE cc_start: 0.7471 (t80) cc_final: 0.6929 (t80) REVERT: A 277 MET cc_start: 0.8947 (mmp) cc_final: 0.8703 (mmp) REVERT: A 395 MET cc_start: 0.7432 (mtt) cc_final: 0.7223 (mtp) REVERT: A 404 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8908 (p) REVERT: A 416 TYR cc_start: 0.8097 (p90) cc_final: 0.7880 (p90) REVERT: B 36 LEU cc_start: 0.7289 (mm) cc_final: 0.6982 (mm) REVERT: B 83 ASP cc_start: 0.8100 (t0) cc_final: 0.7889 (t0) REVERT: B 279 CYS cc_start: 0.8162 (p) cc_final: 0.7883 (p) REVERT: B 303 MET cc_start: 0.5415 (mmm) cc_final: 0.4448 (mmt) REVERT: B 399 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6792 (p) outliers start: 14 outliers final: 7 residues processed: 93 average time/residue: 0.0875 time to fit residues: 11.6322 Evaluate side-chains 84 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 404 SER 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 431 THR Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 0.0270 overall best weight: 0.8042 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.155953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.119929 restraints weight = 25245.690| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 7.23 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4520 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= 0.127 Angle : 0.619 14.989 11033 Z= 0.318 Chirality : 0.042 0.232 1206 Planarity : 0.004 0.057 1244 Dihedral : 19.704 177.530 1453 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.73 % Allowed : 15.71 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.30), residues: 827 helix: 2.04 (0.32), residues: 284 sheet: -0.36 (0.46), residues: 145 loop : -1.67 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.014 0.001 TYR A 416 PHE 0.010 0.001 PHE A 332 TRP 0.028 0.001 TRP A 319 HIS 0.004 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8035) covalent geometry : angle 0.61885 (11033) hydrogen bonds : bond 0.03194 ( 284) hydrogen bonds : angle 4.02413 ( 796) *********************** 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 92 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 273 PHE cc_start: 0.7366 (t80) cc_final: 0.6854 (t80) REVERT: A 395 MET cc_start: 0.7262 (mtt) cc_final: 0.7047 (mtp) REVERT: A 404 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8988 (p) REVERT: B 36 LEU cc_start: 0.7183 (mm) cc_final: 0.6843 (mm) REVERT: B 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7792 (t0) REVERT: B 279 CYS cc_start: 0.8096 (p) cc_final: 0.7821 (p) REVERT: B 399 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6490 (p) outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.0917 time to fit residues: 11.1792 Evaluate side-chains 85 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 404 SER 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 431 THR Chi-restraints excluded: chain B residue 460 LEU 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 38 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.155680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.119706 restraints weight = 25151.693| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 7.20 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4679 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= 0.132 Angle : 0.637 13.838 11033 Z= 0.326 Chirality : 0.042 0.238 1206 Planarity : 0.004 0.057 1244 Dihedral : 19.695 178.111 1453 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.53 % Allowed : 15.18 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.30), residues: 827 helix: 2.09 (0.31), residues: 285 sheet: -0.39 (0.45), residues: 145 loop : -1.64 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.011 0.001 TYR A 210 PHE 0.011 0.001 PHE B 304 TRP 0.030 0.001 TRP A 319 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8035) covalent geometry : angle 0.63695 (11033) hydrogen bonds : bond 0.03244 ( 284) hydrogen bonds : angle 4.01243 ( 796) *********************** 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 94 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8806 (tt) REVERT: A 273 PHE cc_start: 0.7363 (t80) cc_final: 0.6965 (t80) REVERT: A 277 MET cc_start: 0.8782 (mmp) cc_final: 0.8568 (mmp) REVERT: A 324 SER cc_start: 0.7495 (OUTLIER) cc_final: 0.7181 (p) REVERT: A 328 LYS cc_start: 0.8490 (mttm) cc_final: 0.8129 (mttp) REVERT: A 395 MET cc_start: 0.7344 (mtt) cc_final: 0.7138 (mtp) REVERT: A 404 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8998 (p) REVERT: B 36 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6880 (mm) REVERT: B 83 ASP cc_start: 0.8144 (t0) cc_final: 0.7818 (t0) REVERT: B 279 CYS cc_start: 0.8135 (p) cc_final: 0.7806 (p) REVERT: B 303 MET cc_start: 0.5047 (mmm) cc_final: 0.3473 (mmt) REVERT: B 399 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6361 (p) outliers start: 19 outliers final: 11 residues processed: 85 average time/residue: 0.0810 time to fit residues: 10.0399 Evaluate side-chains 87 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 36 LEU 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 431 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 42 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.140143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.106957 restraints weight = 22226.359| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 6.44 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8035 Z= 0.306 Angle : 0.814 9.509 11033 Z= 0.424 Chirality : 0.050 0.300 1206 Planarity : 0.005 0.070 1244 Dihedral : 19.886 178.247 1453 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.22 % Favored : 91.66 % Rotamer: Outliers : 3.33 % Allowed : 14.91 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.29), residues: 827 helix: 1.49 (0.32), residues: 286 sheet: -0.98 (0.44), residues: 144 loop : -1.80 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 209 TYR 0.020 0.003 TYR B 115 PHE 0.026 0.003 PHE B 304 TRP 0.035 0.002 TRP A 319 HIS 0.008 0.002 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 8035) covalent geometry : angle 0.81426 (11033) hydrogen bonds : bond 0.05323 ( 284) hydrogen bonds : angle 4.81725 ( 796) *********************** 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 98 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7938 (t80) cc_final: 0.7557 (t80) REVERT: A 227 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8689 (tt) REVERT: A 324 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7208 (p) REVERT: A 387 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5270 (p0) REVERT: A 404 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8977 (p) REVERT: B 36 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7285 (mm) REVERT: B 263 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (mptt) REVERT: B 303 MET cc_start: 0.5363 (mmm) cc_final: 0.3568 (mmt) outliers start: 25 outliers final: 15 residues processed: 87 average time/residue: 0.0795 time to fit residues: 10.1228 Evaluate side-chains 90 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 317 VAL 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 491 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 0.0470 chunk 76 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.114176 restraints weight = 21560.951| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 6.52 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.5348 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= 0.139 Angle : 0.656 13.443 11033 Z= 0.340 Chirality : 0.043 0.256 1206 Planarity : 0.004 0.065 1244 Dihedral : 19.829 178.009 1453 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 2.13 % Allowed : 16.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.29), residues: 827 helix: 1.75 (0.32), residues: 286 sheet: -0.60 (0.44), residues: 143 loop : -1.72 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.011 0.001 TYR A 392 PHE 0.014 0.001 PHE A 273 TRP 0.043 0.002 TRP A 319 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8035) covalent geometry : angle 0.65636 (11033) hydrogen bonds : bond 0.03449 ( 284) hydrogen bonds : angle 4.31260 ( 796) ********************** 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 97 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8729 (tt) REVERT: A 404 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.8919 (p) REVERT: A 411 LYS cc_start: 0.8376 (tmtt) cc_final: 0.8144 (tptp) REVERT: B 36 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6708 (mm) REVERT: B 83 ASP cc_start: 0.7913 (t0) cc_final: 0.7652 (t0) REVERT: B 303 MET cc_start: 0.5557 (mmm) cc_final: 0.5171 (mmm) REVERT: B 316 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7519 (pp20) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.0832 time to fit residues: 10.7520 Evaluate side-chains 89 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 460 LEU 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 86 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.143814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.111332 restraints weight = 21916.569| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 6.35 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5555 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= 0.186 Angle : 0.692 10.210 11033 Z= 0.358 Chirality : 0.044 0.267 1206 Planarity : 0.004 0.063 1244 Dihedral : 19.831 178.865 1453 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.00 % Allowed : 16.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.29), residues: 827 helix: 1.78 (0.32), residues: 284 sheet: -0.72 (0.47), residues: 125 loop : -1.68 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.034 0.002 TYR A 210 PHE 0.025 0.002 PHE A 198 TRP 0.037 0.002 TRP A 319 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8035) covalent geometry : angle 0.69161 (11033) hydrogen bonds : bond 0.03824 ( 284) hydrogen bonds : angle 4.38583 ( 796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.31 seconds wall clock time: 40 minutes 42.32 seconds (2442.32 seconds total)