Starting phenix.real_space_refine on Thu Jul 2 09:08:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8squ_40713/07_2026/8squ_40713_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8squ_40713/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8squ_40713/07_2026/8squ_40713_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8squ_40713/07_2026/8squ_40713_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8squ_40713/07_2026/8squ_40713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8squ_40713/07_2026/8squ_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-dev-6108/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: 1.94, per 1000 atoms: 0.25 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: 0.73 Conformation dependent library (CDL) restraints added in 294.0 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: 0.72 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: 1.22 Time building geometry restraints manager: 0.97 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: 10793 2.00 - 4.00: 201 4.00 - 5.99: 33 5.99 - 7.99: 5 7.99 - 9.99: 1 Bond angle restraints: 11033 Sorted by residual: 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 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+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: 1153 0.105 - 0.210: 47 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.210 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- 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= 0.233 Angle : 0.648 9.991 11033 Z= 0.406 Chirality : 0.055 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 0.00350 / 0.23 ( 8035) covalent geometry : angle 0.64777 / 0.41 (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 : 0.285 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: 0.7875 (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: 0.1035 time to fit residues: 25.1541 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 : 0.283 ------------------------------------------------------------------------------- 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... ** 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 = 0.4691 r_free = 0.4691 target = 0.161384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.124657 restraints weight = 24508.652| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 7.25 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2196 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= 0.154 Angle : 0.698 10.610 11033 Z= 0.370 Chirality : 0.049 0.319 1206 Planarity : 0.004 0.054 1244 Dihedral : 19.230 177.444 1453 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.07 % Allowed : 11.05 % 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: -0.39 (0.29), residues: 827 helix: 1.86 (0.32), residues: 275 sheet: -0.45 (0.48), residues: 131 loop : -1.74 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.019 0.002 TYR B 56 PHE 0.021 0.002 PHE B 93 TRP 0.020 0.001 TRP B 86 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8035) covalent geometry : angle 0.69810 / 0.37 (11033) hydrogen bonds : bond 0.04343 / 2.88 ( 284) hydrogen bonds : angle 5.11327 / 3.59 ( 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 114 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.290 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: 0.8905 (mp0) cc_final: 0.8372 (pm20) REVERT: A 210 TYR cc_start: 0.7940 (t80) cc_final: 0.7728 (t80) REVERT: A 273 PHE cc_start: 0.7324 (t80) cc_final: 0.6862 (t80) REVERT: A 277 MET cc_start: 0.8779 (mmp) cc_final: 0.8552 (mmp) REVERT: A 416 TYR cc_start: 0.7640 (p90) cc_final: 0.7032 (p90) REVERT: B 83 ASP cc_start: 0.8077 (t0) cc_final: 0.7699 (t0) REVERT: B 226 GLU cc_start: 0.7793 (tt0) cc_final: 0.7196 (mt-10) REVERT: B 303 MET cc_start: 0.4816 (mmp) cc_final: 0.4044 (mmp) REVERT: B 396 LEU cc_start: 0.6905 (mt) cc_final: 0.6127 (mp) outliers start: 8 outliers final: 5 residues processed: 109 average time/residue: 0.0792 time to fit residues: 12.2051 Evaluate side-chains 89 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.114610 restraints weight = 21240.063| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 6.12 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8035 Z= 0.245 Angle : 0.747 12.667 11033 Z= 0.393 Chirality : 0.051 0.363 1206 Planarity : 0.004 0.053 1244 Dihedral : 19.343 177.921 1453 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % 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: -0.60 (0.30), residues: 827 helix: 1.47 (0.32), residues: 284 sheet: -0.68 (0.45), residues: 154 loop : -1.76 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 213 TYR 0.015 0.002 TYR A 225 PHE 0.021 0.002 PHE A 223 TRP 0.010 0.001 TRP B 370 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.25 ( 8035) covalent geometry : angle 0.74693 / 0.39 (11033) hydrogen bonds : bond 0.04764 / 3.04 ( 284) hydrogen bonds : angle 4.92434 / 3.53 ( 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: 16 poor density : 89 time to evaluate : 0.282 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: 0.8793 (mp0) cc_final: 0.8376 (pm20) REVERT: A 210 TYR cc_start: 0.7963 (t80) cc_final: 0.7551 (t80) REVERT: A 277 MET cc_start: 0.8972 (mmp) cc_final: 0.8687 (mmp) REVERT: A 339 SER cc_start: 0.8523 (m) cc_final: 0.8129 (t) REVERT: B 83 ASP cc_start: 0.7978 (t0) cc_final: 0.7690 (t0) outliers start: 16 outliers final: 8 residues processed: 99 average time/residue: 0.0834 time to fit residues: 11.7459 Evaluate side-chains 83 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS 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 423 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.0170 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 24 optimal weight: 1.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4561 r_free = 0.4561 target = 0.150751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.117183 restraints weight = 21310.444| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 6.39 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3111 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= 0.143 Angle : 0.642 10.271 11033 Z= 0.341 Chirality : 0.048 0.346 1206 Planarity : 0.004 0.051 1244 Dihedral : 19.377 178.320 1453 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.86 % Allowed : 14.91 % 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: -0.45 (0.29), residues: 827 helix: 1.72 (0.32), residues: 283 sheet: -0.62 (0.47), residues: 139 loop : -1.73 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 257 TYR 0.014 0.001 TYR A 225 PHE 0.016 0.002 PHE B 313 TRP 0.010 0.001 TRP B 370 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 8035) covalent geometry : angle 0.64175 / 0.34 (11033) hydrogen bonds : bond 0.03718 / 2.43 ( 284) hydrogen bonds : angle 4.66649 / 3.36 ( 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 102 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.310 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: 0.8687 (mp0) cc_final: 0.8355 (pm20) REVERT: A 210 TYR cc_start: 0.7890 (t80) cc_final: 0.6925 (t80) REVERT: A 227 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8860 (tt) REVERT: A 273 PHE cc_start: 0.7327 (t80) cc_final: 0.6863 (t80) REVERT: A 339 SER cc_start: 0.8513 (m) cc_final: 0.8110 (t) REVERT: A 387 ASP cc_start: 0.5103 (OUTLIER) cc_final: 0.4899 (p0) REVERT: B 83 ASP cc_start: 0.7913 (t0) cc_final: 0.7665 (t0) REVERT: B 226 GLU cc_start: 0.7760 (tt0) cc_final: 0.7142 (mt-10) REVERT: B 303 MET cc_start: 0.5908 (mmm) cc_final: 0.5648 (mmm) REVERT: B 399 THR cc_start: 0.6812 (OUTLIER) cc_final: 0.6521 (p) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.0844 time to fit residues: 11.1331 Evaluate side-chains 88 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 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: 0.0570 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.152300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.118876 restraints weight = 21229.797| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 6.41 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3302 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= 0.124 Angle : 0.625 12.310 11033 Z= 0.331 Chirality : 0.047 0.331 1206 Planarity : 0.004 0.053 1244 Dihedral : 19.406 178.752 1453 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.13 % Allowed : 15.05 % 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: -0.39 (0.29), residues: 827 helix: 1.85 (0.32), residues: 282 sheet: -0.61 (0.46), residues: 137 loop : -1.73 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.016 0.001 TYR A 210 PHE 0.013 0.001 PHE A 273 TRP 0.012 0.001 TRP B 370 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8035) covalent geometry : angle 0.62537 / 0.33 (11033) hydrogen bonds : bond 0.03397 / 2.30 ( 284) hydrogen bonds : angle 4.48553 / 3.24 ( 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 102 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.281 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: 0.8661 (mp0) cc_final: 0.8363 (pm20) REVERT: A 210 TYR cc_start: 0.7941 (t80) cc_final: 0.7149 (t80) REVERT: A 273 PHE cc_start: 0.7443 (t80) cc_final: 0.7012 (t80) REVERT: A 309 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6797 (tpt) REVERT: A 339 SER cc_start: 0.8583 (m) cc_final: 0.8104 (t) REVERT: A 387 ASP cc_start: 0.5136 (OUTLIER) cc_final: 0.4903 (p0) REVERT: A 416 TYR cc_start: 0.7967 (p90) cc_final: 0.7402 (p90) REVERT: B 83 ASP cc_start: 0.7899 (t0) cc_final: 0.7664 (t0) REVERT: B 226 GLU cc_start: 0.7714 (tt0) cc_final: 0.7097 (mt-10) REVERT: B 303 MET cc_start: 0.5884 (mmm) cc_final: 0.5657 (mmm) REVERT: B 399 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6374 (p) outliers start: 16 outliers final: 8 residues processed: 93 average time/residue: 0.0778 time to fit residues: 10.3691 Evaluate side-chains 87 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 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 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: 0.7980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 0.0060 chunk 20 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 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 = 0.4579 r_free = 0.4579 target = 0.151893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.118938 restraints weight = 21070.821| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 6.18 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8035 Z= 0.126 Angle : 0.611 13.636 11033 Z= 0.324 Chirality : 0.046 0.325 1206 Planarity : 0.004 0.056 1244 Dihedral : 19.471 179.103 1453 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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 are not related in a simple way. whole: -0.33 (0.29), residues: 827 helix: 1.93 (0.32), residues: 282 sheet: -0.46 (0.44), residues: 145 loop : -1.78 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.011 0.001 TYR A 210 PHE 0.012 0.001 PHE B 82 TRP 0.024 0.001 TRP A 319 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8035) covalent geometry : angle 0.61116 / 0.32 (11033) hydrogen bonds : bond 0.03483 / 2.33 ( 284) hydrogen bonds : angle 4.35885 / 3.17 ( 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 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.292 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: 0.8628 (mp0) cc_final: 0.8377 (pm20) REVERT: A 273 PHE cc_start: 0.7442 (t80) cc_final: 0.7013 (t80) REVERT: A 309 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6810 (tpp) REVERT: A 339 SER cc_start: 0.8591 (m) cc_final: 0.8116 (t) REVERT: A 387 ASP cc_start: 0.5172 (OUTLIER) cc_final: 0.4934 (p0) REVERT: B 82 PHE cc_start: 0.7411 (m-80) cc_final: 0.7075 (m-80) REVERT: B 83 ASP cc_start: 0.7881 (t0) cc_final: 0.7671 (t0) REVERT: B 226 GLU cc_start: 0.7750 (tt0) cc_final: 0.7049 (mt-10) REVERT: B 399 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6366 (p) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.0827 time to fit residues: 10.0709 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 50 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 476 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 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 = 0.4548 r_free = 0.4548 target = 0.149818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.116723 restraints weight = 21402.882| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 6.38 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3654 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 : 0.630 10.853 11033 Z= 0.334 Chirality : 0.046 0.331 1206 Planarity : 0.004 0.059 1244 Dihedral : 19.507 179.244 1453 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.26 % Allowed : 15.71 % Favored : 82.02 % 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: -0.43 (0.29), residues: 827 helix: 1.90 (0.32), residues: 283 sheet: -0.54 (0.46), residues: 140 loop : -1.88 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.024 0.002 TYR A 210 PHE 0.017 0.002 PHE B 82 TRP 0.014 0.001 TRP A 319 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 8035) covalent geometry : angle 0.63044 / 0.33 (11033) hydrogen bonds : bond 0.03720 / 2.43 ( 284) hydrogen bonds : angle 4.33757 / 3.17 ( 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: 17 poor density : 80 time to evaluate : 0.299 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: 0.8647 (mp0) cc_final: 0.8410 (pm20) REVERT: A 227 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 273 PHE cc_start: 0.7553 (t80) cc_final: 0.7141 (t80) REVERT: A 339 SER cc_start: 0.8505 (m) cc_final: 0.8087 (t) REVERT: A 387 ASP cc_start: 0.5167 (OUTLIER) cc_final: 0.4912 (p0) REVERT: B 82 PHE cc_start: 0.7514 (m-80) cc_final: 0.7134 (m-80) REVERT: B 83 ASP cc_start: 0.7869 (t0) cc_final: 0.7665 (t0) REVERT: B 303 MET cc_start: 0.5583 (mmm) cc_final: 0.4610 (mmt) REVERT: B 407 ARG cc_start: 0.7189 (ttt-90) cc_final: 0.5637 (ptp-110) REVERT: B 417 SER cc_start: 0.8827 (t) cc_final: 0.8568 (p) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.0867 time to fit residues: 10.6167 Evaluate side-chains 90 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 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 431 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 476 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 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 = 0.4566 r_free = 0.4566 target = 0.151035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.117871 restraints weight = 21192.300| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 6.27 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3753 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= 0.125 Angle : 0.618 10.589 11033 Z= 0.327 Chirality : 0.046 0.317 1206 Planarity : 0.004 0.060 1244 Dihedral : 19.533 178.738 1453 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.26 % Allowed : 16.11 % Favored : 81.62 % 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: -0.34 (0.29), residues: 827 helix: 1.99 (0.32), residues: 283 sheet: -0.53 (0.45), residues: 140 loop : -1.84 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.017 0.001 TYR A 210 PHE 0.014 0.001 PHE A 273 TRP 0.015 0.001 TRP A 319 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8035) covalent geometry : angle 0.61827 / 0.33 (11033) hydrogen bonds : bond 0.03391 / 2.25 ( 284) hydrogen bonds : angle 4.30334 / 3.15 ( 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 95 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.187 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: 0.8635 (mp0) cc_final: 0.8429 (pm20) REVERT: A 227 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8724 (tt) REVERT: A 273 PHE cc_start: 0.7471 (t80) cc_final: 0.7008 (t80) REVERT: A 277 MET cc_start: 0.8703 (mmp) cc_final: 0.8468 (mmp) REVERT: A 339 SER cc_start: 0.8483 (m) cc_final: 0.8062 (t) REVERT: A 387 ASP cc_start: 0.5257 (OUTLIER) cc_final: 0.5012 (p0) REVERT: B 82 PHE cc_start: 0.7472 (m-80) cc_final: 0.7069 (m-80) REVERT: B 83 ASP cc_start: 0.7955 (t0) cc_final: 0.7723 (t0) REVERT: B 86 TRP cc_start: 0.6724 (t60) cc_final: 0.6495 (t60) REVERT: B 303 MET cc_start: 0.5674 (mmm) cc_final: 0.5422 (mmm) REVERT: B 399 THR cc_start: 0.6711 (OUTLIER) cc_final: 0.6452 (p) REVERT: B 417 SER cc_start: 0.8833 (t) cc_final: 0.8619 (p) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.0591 time to fit residues: 7.4169 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 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 439 ASN Chi-restraints excluded: chain B residue 476 GLU 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: 0.0770 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 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 = 0.4546 r_free = 0.4546 target = 0.149572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.116513 restraints weight = 21227.547| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 6.25 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8035 Z= 0.154 Angle : 0.626 9.466 11033 Z= 0.332 Chirality : 0.046 0.320 1206 Planarity : 0.004 0.063 1244 Dihedral : 19.579 178.725 1453 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.00 % Allowed : 16.11 % Favored : 81.89 % 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: 1.94 (0.32), residues: 284 sheet: -0.59 (0.45), residues: 140 loop : -1.89 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.010 0.001 TYR A 225 PHE 0.013 0.001 PHE A 223 TRP 0.012 0.001 TRP A 319 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8035) covalent geometry : angle 0.62614 / 0.33 (11033) hydrogen bonds : bond 0.03582 / 2.35 ( 284) hydrogen bonds : angle 4.31804 / 3.18 ( 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 95 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8684 (mp0) cc_final: 0.8476 (pm20) REVERT: A 227 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8750 (tt) REVERT: A 273 PHE cc_start: 0.7501 (t80) cc_final: 0.7053 (t80) REVERT: A 277 MET cc_start: 0.8785 (mmp) cc_final: 0.8519 (mmp) REVERT: A 339 SER cc_start: 0.8484 (m) cc_final: 0.8057 (t) REVERT: A 387 ASP cc_start: 0.4985 (OUTLIER) cc_final: 0.4710 (p0) REVERT: B 82 PHE cc_start: 0.7569 (m-80) cc_final: 0.7292 (m-80) REVERT: B 83 ASP cc_start: 0.8002 (t0) cc_final: 0.7761 (t0) REVERT: B 399 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.6471 (p) REVERT: B 417 SER cc_start: 0.8895 (t) cc_final: 0.8683 (p) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.0635 time to fit residues: 7.9763 Evaluate side-chains 92 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 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 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 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: 0.3980 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 0.0020 chunk 76 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 overall best weight: 0.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 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 = 0.4579 r_free = 0.4579 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.118761 restraints weight = 20976.612| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 6.22 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8035 Z= 0.124 Angle : 0.638 10.031 11033 Z= 0.336 Chirality : 0.046 0.304 1206 Planarity : 0.004 0.062 1244 Dihedral : 19.627 178.343 1453 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.86 % Allowed : 16.11 % Favored : 82.02 % 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: -0.44 (0.29), residues: 827 helix: 1.87 (0.32), residues: 286 sheet: -0.56 (0.45), residues: 140 loop : -1.89 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.018 0.001 TYR A 416 PHE 0.014 0.001 PHE B 419 TRP 0.016 0.001 TRP A 319 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8035) covalent geometry : angle 0.63759 / 0.34 (11033) hydrogen bonds : bond 0.03248 / 2.19 ( 284) hydrogen bonds : angle 4.28316 / 3.15 ( 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 94 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8775 (tt) REVERT: A 273 PHE cc_start: 0.7350 (t80) cc_final: 0.6923 (t80) REVERT: A 277 MET cc_start: 0.8706 (mmp) cc_final: 0.8497 (mmp) REVERT: A 339 SER cc_start: 0.8507 (m) cc_final: 0.8075 (t) REVERT: A 387 ASP cc_start: 0.5101 (OUTLIER) cc_final: 0.4828 (p0) REVERT: B 82 PHE cc_start: 0.7456 (m-80) cc_final: 0.7083 (m-80) REVERT: B 83 ASP cc_start: 0.7954 (t0) cc_final: 0.7645 (t0) REVERT: B 215 LEU cc_start: 0.7965 (mt) cc_final: 0.7756 (mm) REVERT: B 303 MET cc_start: 0.5512 (mmm) cc_final: 0.4553 (mmt) REVERT: B 399 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6393 (p) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.0852 time to fit residues: 10.5680 Evaluate side-chains 89 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 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 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 86 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** 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 = 0.4488 r_free = 0.4488 target = 0.145083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.111909 restraints weight = 21838.578| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 6.26 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8035 Z= 0.284 Angle : 0.752 9.094 11033 Z= 0.402 Chirality : 0.051 0.368 1206 Planarity : 0.005 0.073 1244 Dihedral : 19.689 179.063 1453 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 2.00 % Allowed : 16.38 % Favored : 81.62 % 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: -0.78 (0.29), residues: 827 helix: 1.55 (0.32), residues: 286 sheet: -0.89 (0.44), residues: 155 loop : -2.02 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 213 TYR 0.018 0.002 TYR A 171 PHE 0.030 0.003 PHE A 223 TRP 0.021 0.002 TRP B 86 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 ( 8035) covalent geometry : angle 0.75229 / 0.40 (11033) hydrogen bonds : bond 0.04780 / 3.01 ( 284) hydrogen bonds : angle 4.56752 / 3.38 ( 796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2099.66 seconds wall clock time: 36 minutes 48.50 seconds (2208.50 seconds total)