Starting phenix.real_space_refine on Wed Aug 5 01:34:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8squ_40713/08_2026/8squ_40713_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8squ_40713/08_2026/8squ_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_40713/08_2026/8squ_40713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2026/8squ_40713.map" model { file = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2026/8squ_40713_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8squ_40713/08_2026/8squ_40713_neut.cif" } 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-2.2rc3-6140/lib/python3.11/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: 1.80, per 1000 atoms: 0.23 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: 0.71 Conformation dependent library (CDL) restraints added in 337.2 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: 0.76 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: 1.02 Time building geometry restraints manager: 0.94 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=" C3' DT D 12 " pdb=" C2' DT D 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.435 1.468 -0.033 1.30e-02 5.92e+03 6.54e+00 bond pdb=" C3' DG D 15 " pdb=" C2' DG D 15 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.49e+00 bond pdb=" C3' DC D 18 " pdb=" C2' DC D 18 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.05e+00 bond pdb=" C1' DC D 18 " pdb=" N1 DC D 18 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.53e+00 ... (remaining 8030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10762 2.00 - 4.00: 233 4.00 - 5.99: 32 5.99 - 7.99: 5 7.99 - 9.99: 1 Bond angle restraints: 11033 Sorted by residual: 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 7.00e-01 2.04e+00 1.92e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 21 " pdb=" C4 DT D 21 " pdb=" O4 DT D 21 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 ... (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: 1143 0.105 - 0.210: 57 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: 1.100 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 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 : 0.004 0.040 8035 Z= 0.238 Angle : 0.661 9.991 11033 Z= 0.426 Chirality : 0.056 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 are 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/Z covalent geometry : bond 0.00352 / 0.24 ( 8035) covalent geometry : angle 0.66115 / 0.43 (11033) hydrogen bonds : bond 0.17918 / 11.57 ( 284) hydrogen bonds : angle 6.78074 / 4.78 ( 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 : 0.207 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: 0.8278 (m-30) cc_final: 0.7876 (m-30) REVERT: B 303 MET cc_start: 0.4240 (mmp) cc_final: 0.2826 (tpt) REVERT: B 396 LEU cc_start: 0.6911 (mt) cc_final: 0.6114 (mt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0910 time to fit residues: 22.1801 Evaluate side-chains 89 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.161549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.125031 restraints weight = 24508.025| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 7.22 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2224 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= 0.152 Angle : 0.701 10.896 11033 Z= 0.371 Chirality : 0.048 0.310 1206 Planarity : 0.004 0.055 1244 Dihedral : 19.200 177.674 1453 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.93 % Allowed : 11.19 % Favored : 87.88 % 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 are not related in a simple way. whole: -0.42 (0.29), residues: 827 helix: 1.85 (0.32), residues: 275 sheet: -0.54 (0.47), residues: 139 loop : -1.75 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 374 TYR 0.018 0.002 TYR B 56 PHE 0.018 0.002 PHE B 93 TRP 0.018 0.001 TRP A 319 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8035) covalent geometry : angle 0.70092 / 0.37 (11033) hydrogen bonds : bond 0.04268 / 2.83 ( 284) hydrogen bonds : angle 5.10299 / 3.58 ( 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 113 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8896 (mp0) cc_final: 0.8383 (pm20) REVERT: A 210 TYR cc_start: 0.7935 (t80) cc_final: 0.7065 (t80) REVERT: A 273 PHE cc_start: 0.7319 (t80) cc_final: 0.6846 (t80) REVERT: A 277 MET cc_start: 0.8766 (mmp) cc_final: 0.8536 (mmp) REVERT: A 416 TYR cc_start: 0.7675 (p90) cc_final: 0.7139 (p90) REVERT: B 82 PHE cc_start: 0.7485 (m-80) cc_final: 0.7255 (m-80) REVERT: B 83 ASP cc_start: 0.8089 (t0) cc_final: 0.7715 (t0) REVERT: B 226 GLU cc_start: 0.7795 (tt0) cc_final: 0.7201 (mt-10) REVERT: B 303 MET cc_start: 0.4815 (mmp) cc_final: 0.4054 (mmp) REVERT: B 396 LEU cc_start: 0.6906 (mt) cc_final: 0.6126 (mp) outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.0645 time to fit residues: 10.0027 Evaluate side-chains 88 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 274 VAL 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: 8.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.0040 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 439 ASN ** 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 = 0.4587 r_free = 0.4587 target = 0.150824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.118580 restraints weight = 21123.790| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 6.16 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8035 Z= 0.170 Angle : 0.669 9.309 11033 Z= 0.353 Chirality : 0.047 0.339 1206 Planarity : 0.004 0.051 1244 Dihedral : 19.180 177.349 1453 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.13 % Allowed : 13.32 % Favored : 84.55 % 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 are not related in a simple way. whole: -0.40 (0.30), residues: 827 helix: 1.75 (0.32), residues: 283 sheet: -0.49 (0.47), residues: 139 loop : -1.72 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.019 0.002 TYR A 210 PHE 0.015 0.002 PHE A 380 TRP 0.010 0.001 TRP B 370 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 8035) covalent geometry : angle 0.66908 / 0.35 (11033) hydrogen bonds : bond 0.04066 / 2.68 ( 284) hydrogen bonds : angle 4.76657 / 3.40 ( 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 107 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.195 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: 0.8683 (mp0) cc_final: 0.8259 (pm20) REVERT: A 210 TYR cc_start: 0.8039 (t80) cc_final: 0.7131 (t80) REVERT: A 273 PHE cc_start: 0.7403 (t80) cc_final: 0.6874 (t80) REVERT: A 277 MET cc_start: 0.8919 (mmp) cc_final: 0.8653 (mmp) REVERT: A 339 SER cc_start: 0.8425 (m) cc_final: 0.8047 (t) REVERT: A 416 TYR cc_start: 0.7867 (p90) cc_final: 0.7267 (p90) REVERT: B 82 PHE cc_start: 0.7466 (m-80) cc_final: 0.7170 (m-80) REVERT: B 83 ASP cc_start: 0.8016 (t0) cc_final: 0.7633 (t0) REVERT: B 226 GLU cc_start: 0.7807 (tt0) cc_final: 0.7132 (mt-10) REVERT: B 399 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6375 (p) outliers start: 16 outliers final: 8 residues processed: 101 average time/residue: 0.0637 time to fit residues: 9.1663 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 TYR 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 476 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.0000 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.153820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.121015 restraints weight = 20906.681| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 6.33 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8035 Z= 0.129 Angle : 0.629 10.194 11033 Z= 0.332 Chirality : 0.045 0.307 1206 Planarity : 0.004 0.048 1244 Dihedral : 19.246 176.299 1453 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.46 % Allowed : 13.72 % 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 are not related in a simple way. whole: -0.35 (0.30), residues: 827 helix: 1.83 (0.32), residues: 283 sheet: -0.40 (0.49), residues: 132 loop : -1.73 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.021 0.002 TYR B 56 PHE 0.013 0.001 PHE B 313 TRP 0.010 0.001 TRP B 370 HIS 0.007 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 8035) covalent geometry : angle 0.62935 / 0.33 (11033) hydrogen bonds : bond 0.03557 / 2.37 ( 284) hydrogen bonds : angle 4.54014 / 3.25 ( 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 100 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8747 (mp0) cc_final: 0.8356 (pm20) REVERT: A 210 TYR cc_start: 0.8003 (t80) cc_final: 0.7007 (t80) REVERT: A 273 PHE cc_start: 0.7407 (t80) cc_final: 0.6919 (t80) REVERT: A 277 MET cc_start: 0.8920 (mmp) cc_final: 0.8621 (mmp) REVERT: A 339 SER cc_start: 0.8349 (m) cc_final: 0.7956 (t) REVERT: A 395 MET cc_start: 0.7590 (mtp) cc_final: 0.7366 (mtt) REVERT: A 416 TYR cc_start: 0.7804 (p90) cc_final: 0.7341 (p90) REVERT: B 82 PHE cc_start: 0.7308 (m-80) cc_final: 0.7014 (m-80) REVERT: B 83 ASP cc_start: 0.8041 (t0) cc_final: 0.7681 (t0) REVERT: B 226 GLU cc_start: 0.7763 (tt0) cc_final: 0.7110 (mt-10) REVERT: B 399 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6398 (p) outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 0.0659 time to fit residues: 8.9889 Evaluate side-chains 87 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 274 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 476 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.120900 restraints weight = 20926.405| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 6.32 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3245 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= 0.124 Angle : 0.610 12.594 11033 Z= 0.321 Chirality : 0.045 0.317 1206 Planarity : 0.003 0.052 1244 Dihedral : 19.281 178.873 1453 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.46 % Allowed : 14.91 % Favored : 83.62 % 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 are not related in a simple way. whole: -0.29 (0.30), residues: 827 helix: 1.95 (0.32), residues: 283 sheet: -0.33 (0.46), residues: 140 loop : -1.81 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.014 0.001 TYR B 56 PHE 0.010 0.001 PHE A 198 TRP 0.024 0.001 TRP A 319 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8035) covalent geometry : angle 0.60969 / 0.32 (11033) hydrogen bonds : bond 0.03458 / 2.34 ( 284) hydrogen bonds : angle 4.36064 / 3.16 ( 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 94 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8683 (mp0) cc_final: 0.8355 (pm20) REVERT: A 273 PHE cc_start: 0.7376 (t80) cc_final: 0.6835 (t80) REVERT: A 277 MET cc_start: 0.8947 (mmp) cc_final: 0.8716 (mmp) REVERT: A 339 SER cc_start: 0.8494 (m) cc_final: 0.8048 (t) REVERT: A 416 TYR cc_start: 0.7846 (p90) cc_final: 0.7387 (p90) REVERT: B 82 PHE cc_start: 0.7176 (m-80) cc_final: 0.6883 (m-80) REVERT: B 83 ASP cc_start: 0.8052 (t0) cc_final: 0.7682 (t0) REVERT: B 226 GLU cc_start: 0.7736 (tt0) cc_final: 0.7154 (mt-10) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.0709 time to fit residues: 8.9042 Evaluate side-chains 83 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.153780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.121018 restraints weight = 20866.273| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 6.46 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8035 Z= 0.122 Angle : 0.610 14.084 11033 Z= 0.319 Chirality : 0.044 0.315 1206 Planarity : 0.003 0.053 1244 Dihedral : 19.304 179.287 1453 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.40 % Allowed : 14.51 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.30), residues: 827 helix: 2.00 (0.32), residues: 283 sheet: -0.39 (0.45), residues: 146 loop : -1.79 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.029 0.001 TYR A 210 PHE 0.009 0.001 PHE A 332 TRP 0.011 0.001 TRP B 370 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8035) covalent geometry : angle 0.60981 / 0.32 (11033) hydrogen bonds : bond 0.03367 / 2.28 ( 284) hydrogen bonds : angle 4.25495 / 3.08 ( 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 98 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.163 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: 0.8722 (mp0) cc_final: 0.8404 (pm20) REVERT: A 273 PHE cc_start: 0.7379 (t80) cc_final: 0.6845 (t80) REVERT: A 277 MET cc_start: 0.8940 (mmp) cc_final: 0.8702 (mmp) REVERT: A 339 SER cc_start: 0.8413 (m) cc_final: 0.8028 (t) REVERT: A 416 TYR cc_start: 0.7919 (p90) cc_final: 0.7701 (p90) REVERT: B 82 PHE cc_start: 0.7144 (m-80) cc_final: 0.6914 (m-80) REVERT: B 83 ASP cc_start: 0.8028 (t0) cc_final: 0.7685 (t0) REVERT: B 116 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8351 (t0) REVERT: B 145 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5555 (p0) REVERT: B 226 GLU cc_start: 0.7688 (tt0) cc_final: 0.7125 (mt-10) REVERT: B 279 CYS cc_start: 0.8091 (p) cc_final: 0.7875 (p) REVERT: B 399 THR cc_start: 0.6580 (OUTLIER) cc_final: 0.6332 (p) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 0.0697 time to fit residues: 9.3531 Evaluate side-chains 86 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 145 ASP 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 420 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.152819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.120232 restraints weight = 21060.205| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 6.26 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 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 0.060 8035 Z= 0.130 Angle : 0.607 12.125 11033 Z= 0.317 Chirality : 0.044 0.323 1206 Planarity : 0.004 0.057 1244 Dihedral : 19.329 179.642 1453 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.13 % Allowed : 14.65 % Favored : 83.22 % 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 are not related in a simple way. whole: -0.29 (0.29), residues: 827 helix: 2.00 (0.31), residues: 284 sheet: -0.34 (0.46), residues: 140 loop : -1.85 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 481 TYR 0.025 0.001 TYR A 210 PHE 0.010 0.001 PHE A 332 TRP 0.014 0.001 TRP B 86 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8035) covalent geometry : angle 0.60714 / 0.32 (11033) hydrogen bonds : bond 0.03394 / 2.27 ( 284) hydrogen bonds : angle 4.18793 / 3.04 ( 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 97 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8700 (mp0) cc_final: 0.8461 (pm20) REVERT: A 273 PHE cc_start: 0.7357 (t80) cc_final: 0.6829 (t80) REVERT: A 277 MET cc_start: 0.9002 (mmp) cc_final: 0.8754 (mmp) REVERT: A 339 SER cc_start: 0.8412 (m) cc_final: 0.8023 (t) REVERT: A 416 TYR cc_start: 0.7947 (p90) cc_final: 0.7709 (p90) REVERT: B 82 PHE cc_start: 0.7160 (m-80) cc_final: 0.6935 (m-80) REVERT: B 83 ASP cc_start: 0.8051 (t0) cc_final: 0.7712 (t0) REVERT: B 116 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8469 (t0) REVERT: B 145 ASP cc_start: 0.5789 (OUTLIER) cc_final: 0.5579 (p0) REVERT: B 226 GLU cc_start: 0.7703 (tt0) cc_final: 0.7130 (mt-10) REVERT: B 279 CYS cc_start: 0.7991 (p) cc_final: 0.7757 (p) REVERT: B 303 MET cc_start: 0.5203 (mmm) cc_final: 0.4770 (mmm) REVERT: B 399 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6309 (p) REVERT: B 407 ARG cc_start: 0.7106 (ttt-90) cc_final: 0.5773 (ptm160) outliers start: 16 outliers final: 11 residues processed: 90 average time/residue: 0.0781 time to fit residues: 10.1493 Evaluate side-chains 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 145 ASP 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 420 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.153908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.121391 restraints weight = 20884.401| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 6.40 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8035 Z= 0.119 Angle : 0.600 11.562 11033 Z= 0.315 Chirality : 0.044 0.312 1206 Planarity : 0.004 0.057 1244 Dihedral : 19.370 179.242 1453 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.73 % Allowed : 15.45 % Favored : 82.82 % 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 are not related in a simple way. whole: -0.25 (0.29), residues: 827 helix: 2.03 (0.32), residues: 285 sheet: -0.41 (0.44), residues: 146 loop : -1.82 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.018 0.001 TYR A 210 PHE 0.010 0.001 PHE B 419 TRP 0.018 0.001 TRP B 86 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 8035) covalent geometry : angle 0.60045 / 0.32 (11033) hydrogen bonds : bond 0.03173 / 2.15 ( 284) hydrogen bonds : angle 4.10539 / 2.98 ( 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: 13 poor density : 81 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8724 (mp0) cc_final: 0.8512 (pm20) REVERT: A 273 PHE cc_start: 0.7250 (t80) cc_final: 0.6718 (t80) REVERT: A 416 TYR cc_start: 0.7923 (p90) cc_final: 0.7697 (p90) REVERT: B 82 PHE cc_start: 0.7154 (m-80) cc_final: 0.6803 (m-80) REVERT: B 83 ASP cc_start: 0.8043 (t0) cc_final: 0.7712 (t0) REVERT: B 116 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8381 (t0) REVERT: B 145 ASP cc_start: 0.5733 (OUTLIER) cc_final: 0.5495 (p0) REVERT: B 226 GLU cc_start: 0.7671 (tt0) cc_final: 0.7112 (mt-10) REVERT: B 279 CYS cc_start: 0.8003 (p) cc_final: 0.7772 (p) REVERT: B 303 MET cc_start: 0.5350 (mmm) cc_final: 0.3759 (mmt) REVERT: B 399 THR cc_start: 0.6539 (OUTLIER) cc_final: 0.6291 (p) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.0727 time to fit residues: 9.3325 Evaluate side-chains 88 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 145 ASP 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 420 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 439 ASN 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 32 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.151455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.119111 restraints weight = 20950.425| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 6.26 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8035 Z= 0.156 Angle : 0.632 10.735 11033 Z= 0.332 Chirality : 0.045 0.338 1206 Planarity : 0.004 0.058 1244 Dihedral : 19.365 179.627 1453 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.86 % Allowed : 15.71 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -0.28 (0.29), residues: 827 helix: 2.05 (0.32), residues: 285 sheet: -0.39 (0.45), residues: 140 loop : -1.87 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.018 0.001 TYR A 210 PHE 0.014 0.001 PHE A 223 TRP 0.013 0.001 TRP B 86 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 8035) covalent geometry : angle 0.63241 / 0.33 (11033) hydrogen bonds : bond 0.03475 / 2.28 ( 284) hydrogen bonds : angle 4.11310 / 3.00 ( 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 94 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7468 (t80) cc_final: 0.7050 (t80) REVERT: A 339 SER cc_start: 0.8428 (m) cc_final: 0.8024 (t) REVERT: A 416 TYR cc_start: 0.7956 (p90) cc_final: 0.7719 (p90) REVERT: B 82 PHE cc_start: 0.7249 (m-80) cc_final: 0.7005 (m-80) REVERT: B 83 ASP cc_start: 0.8122 (t0) cc_final: 0.7747 (t0) REVERT: B 116 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8487 (t0) REVERT: B 145 ASP cc_start: 0.5734 (OUTLIER) cc_final: 0.5498 (p0) REVERT: B 226 GLU cc_start: 0.7721 (tt0) cc_final: 0.7148 (mt-10) REVERT: B 279 CYS cc_start: 0.8131 (p) cc_final: 0.7873 (p) REVERT: B 417 SER cc_start: 0.8910 (t) cc_final: 0.8671 (p) outliers start: 14 outliers final: 11 residues processed: 86 average time/residue: 0.0732 time to fit residues: 9.1689 Evaluate side-chains 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 145 ASP 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 420 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 3 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.152260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.119587 restraints weight = 21069.640| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 6.28 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8035 Z= 0.134 Angle : 0.648 10.939 11033 Z= 0.339 Chirality : 0.045 0.321 1206 Planarity : 0.004 0.060 1244 Dihedral : 19.369 179.268 1453 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.73 % Allowed : 16.11 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -0.28 (0.29), residues: 827 helix: 2.06 (0.32), residues: 286 sheet: -0.29 (0.46), residues: 140 loop : -1.93 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.021 0.001 TYR A 210 PHE 0.019 0.001 PHE A 273 TRP 0.015 0.001 TRP B 86 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8035) covalent geometry : angle 0.64807 / 0.34 (11033) hydrogen bonds : bond 0.03263 / 2.15 ( 284) hydrogen bonds : angle 4.12478 / 3.00 ( 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 92 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7459 (t80) cc_final: 0.6989 (t80) REVERT: A 277 MET cc_start: 0.8727 (mmp) cc_final: 0.8347 (mmp) REVERT: A 339 SER cc_start: 0.8436 (m) cc_final: 0.8021 (t) REVERT: A 416 TYR cc_start: 0.7928 (p90) cc_final: 0.7723 (p90) REVERT: B 36 LEU cc_start: 0.8075 (pt) cc_final: 0.6341 (mm) REVERT: B 82 PHE cc_start: 0.7295 (m-80) cc_final: 0.7039 (m-80) REVERT: B 83 ASP cc_start: 0.8049 (t0) cc_final: 0.7745 (t0) REVERT: B 116 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8426 (t0) REVERT: B 145 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5432 (p0) REVERT: B 226 GLU cc_start: 0.7714 (tt0) cc_final: 0.7162 (mt-10) REVERT: B 279 CYS cc_start: 0.8061 (p) cc_final: 0.7816 (p) REVERT: B 399 THR cc_start: 0.6612 (OUTLIER) cc_final: 0.6359 (p) REVERT: B 417 SER cc_start: 0.8891 (t) cc_final: 0.8634 (p) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.0782 time to fit residues: 9.6798 Evaluate side-chains 90 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 145 ASP 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 420 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.152709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.120132 restraints weight = 21111.012| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 6.32 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4046 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= 0.129 Angle : 0.648 10.939 11033 Z= 0.338 Chirality : 0.044 0.320 1206 Planarity : 0.004 0.057 1244 Dihedral : 19.379 179.168 1453 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.73 % Allowed : 15.98 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -0.30 (0.29), residues: 827 helix: 2.07 (0.32), residues: 286 sheet: -0.35 (0.45), residues: 146 loop : -1.98 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 481 TYR 0.017 0.001 TYR A 210 PHE 0.030 0.001 PHE A 198 TRP 0.016 0.001 TRP B 86 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8035) covalent geometry : angle 0.64765 / 0.34 (11033) hydrogen bonds : bond 0.03191 / 2.11 ( 284) hydrogen bonds : angle 4.08509 / 2.97 ( 796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.85 seconds wall clock time: 31 minutes 40.02 seconds (1900.02 seconds total)